US9981922B2 - KDM1A inhibitors for the treatment of disease - Google Patents

KDM1A inhibitors for the treatment of disease Download PDF

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US9981922B2
US9981922B2 US15/043,121 US201615043121A US9981922B2 US 9981922 B2 US9981922 B2 US 9981922B2 US 201615043121 A US201615043121 A US 201615043121A US 9981922 B2 US9981922 B2 US 9981922B2
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fluorophenyl
amino
benzamide
cyclopropyl
mmol
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US20160237043A1 (en
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Hugh Y. Rienhoff, JR.
John M. McCall
Michael Clare
Cassandra Celatka
Amy E. Tapper
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Imago Biosciences Inc
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Imago Biosciences Inc
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Priority to US15/043,121 priority Critical patent/US9981922B2/en
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Assigned to IMAGO BIOSCIENCES, INC. reassignment IMAGO BIOSCIENCES, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: CLARE, MICHAEL, CELATKA, CASSANDRA, TAPPER, AMY E., MCCALL, JOHN M., RIENHOFF, HUGH Y., JR.
Priority to US15/952,073 priority patent/US10519118B2/en
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Priority to US16/672,083 priority patent/US11230534B2/en
Priority to US17/481,649 priority patent/US11773068B2/en
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Definitions

  • the present disclosure relates to new compounds and compositions and their application as pharmaceuticals for the treatment of diseases.
  • KDM1A also known as lysine-specific demethylase 1, LSD1, Flavin-containing Amine Oxidase Domain-Containing Protein, AOF2, BRAF35-HDAC Complex Protein BHC110, FAD-Binding Protein BRAF35-HDAC Complex
  • KDM1A may alter gene expression in cells sufficient to restore their proper physiologic function or that of the tissue, organ or the patient as a whole. This may be achieved either by enhancing transcription of a gene or genes that are pathologically silenced, e.g., as is the case in some cancer cells and heritable diseases, or decreasing transcription of a gene or genes participating in the pathological state.
  • inhibiting KDM1A would be useful for the treatment of diseases such as cancer and heritable diseases such as Wilson disease, cardiomyopathies, and hemoglobinopathies.
  • Gene expression is regulated through the recruitment of the RNA polymerase II transcription apparatus to the DNA template.
  • the probability of this large multi-protein complex arriving near or at the start of DNA transcription and progressing through the entire coding region of a gene is determined in part by specific DNA sequences called promoters and enhancers, modifications of DNA sequence in the vicinity of the start of transcription, proteins bound to DNA and the topology of the DNA template itself.
  • Factors enhancing the probability of RNA synthesis of protein-coding genes are known as transcription factors some of which participate in the transcription of all protein-coding genes and some of which are specific for the transcription of individual genes.
  • transcription control consists of limiting the physical accessibility of the transcriptional regulatory regions to proteins that can activate or complete transcription; proteins bound to promoter or enhancer DNA sequences can occlude activating factors from binding to these DNA sequences resulting in fewer transcription initiations or extension of the activated progressing RNA polymerase complex.
  • topological constraints that do not allow the template DNA to unwind sufficiently to permit the steady progression of RNA polymerase on the template also serve to limit transcription rates.
  • RNA synthesis using a DNA template in vivo modifications of histones proteins that control among other factors the topology of the DNA template for transcription and its accessibility by the RNA polymerase complex.
  • the conglomerate of histones, other proteins, various RNAs and DNA is called chromatin. Both DNA and histones are chemically modified in such a way as to attract and bind or repel other proteins with the effect of enhancing or repressing transcription.
  • epigenetic The modification of DNA and associated RNAs and proteins that influence the regulation of transcription and replication that does not involve substitution of the canonical DNA bases is termed epigenetic. These epigenetic influences involve reversible chemical modifications of the four DNA bases themselves or post-translational chemical changes to the chromatin proteins and RNDs that associate with DNA. These epigenetic processes can play a pivotal role in activating or silencing the expression of a gene; in addition, the epigenetic modifications can be maintained for the life of an organism or can be dynamically modified in response to specific biochemical signals that originate either internally within the cell or extracellularly.
  • chromatin structure at a specific locus can change radically within seconds to permit maximal transcription or chromatin structure can be modified to fully suppress gene expression, a state of chromatin which can be stably maintained over multiple cell divisions and even transgenerationally.
  • cytosine at the 5′ position is a common DNA base modification that is in turn recognized by a class of proteins most often associated with transcriptional repression.
  • histone proteins are chemically modified but with a wider variety of chemical adducts each of which either alone or in combination enhances or represses transcription of nearby genes. These histone modifications include, among others methylation, acetylation, sumoylation, phosphorylation, ubiquitylation, and myristoylation are recognized by other chromatin-associated proteins that in turn influence transcription rates and DNA replication.
  • histone modifications are not permanent but instead are added and removed according to the needs of the cell for specific gene products at specific times during ontogeny, adult life and the changing influences of the environment.
  • specific chemical modifications of histones are each made by classes of enzymes acting at specific sites. These histone-modifying enzymes are in turn subject to tight regulation. These enzymes can potentially be targeted by compounds that inhibit their activity with the consequence of altering gene expression in a therapeutic manner.
  • Histone methylation can occur on any of the three basic amino acid residues—lysine (K), arginine (R), and histidine (H). Methylation of histone H3 on lysines at positions 4 (H3K4), 9 (H3K9), 27 (H3K27), 36 (H3K36) and 79 (H3K79) are among the best studied of histone modifications that influence gene expression. Lysine tri-methylation (Kme3) on histone 3 (H3) at position 4 (H3K4me3) is a histone mark generally associated with activation of gene expression while H3K9me1 or H3K27me3 are associated with the repression of gene transcription.
  • H3K4me1 is associated with DNA enhancers of gene transcription while H3K4me3 is associated with gene promoter activity. Likewise, loss of the methyl group at H3K4 is associated with repression of gene expression. Thus, the addition and removal of methyl groups at H3K4 constitutes a gene transcription switch. It is also evident that lysine can be modified with a mono-, di- or tri-methyl groups, each modification having a different biological effect through the attraction of different proteins recognizing those specific methylation modifications at that site.
  • a critical aspect of the regulation of the state of histone methylation is the recruitment of methyltransferases and demethylases to specific genetic loci.
  • DNA sequence-specific binding proteins including transcription factors are one class of proteins responsible for this recruitment through the assemblage of protein complexes that bind these methyl-transferring enzymes.
  • a well-studied example is the Drosophila melanogaster trithrorax group (TrxG) response elements (TREs) which recruit the H3K4 methyltransferase, TRX, to specific genes via transcription factors that recognize the TRE DNA sequence.
  • the histone methylation marks are recognized by methyl-binding domains in a diverse group of proteins; these domains include PHD fingers, WD40 and ankyrin repeats, CW and PWWP domains, and the Royal superfamily of proteins. These proteins, in turn, determine which additional activities are recruited into chromatin sites and ultimately the state of transcription at a given locus. Indeed, depending on which methyl-recognition protein binds the marked histone, the same methyl-lysine modification can have opposing effects on transcription.
  • H3K4me2 and H3K4me3 are associated with transcriptional activation, but when bound by the PHD-domain-containing co-repressor protein Inhibitor of Growth family member 2 (ING2), an associated histone deacetylase complex is stabilized repressing gene expression.
  • ING2 PHD-domain-containing co-repressor protein Inhibitor of Growth family member 2
  • the ability to alter gene expression selectively by modifying the state of chromatin allows a novel therapeutic strategy to induce or de-repress the expression of genes that can provide a benefit, especially for genes whose expression has been suppressed by pathological mechanism as in the case of some cancers or suppressed by physiologic mechanism but who de-repression can phenotypically suppress mutations in paralogous genes with complementary function.
  • genes within a genome are members of gene families as a consequence of gene duplication. These genes are termed paralogs of one another. Following gene duplication, patterns of expression of two genes will evolve in a distinct manner in part to control the effects of gene dosage. Following gene duplication, random genetic drift arising from naturally occurring mutations and the subsequent selection of nucleotide sequence is commonly observed first in non-coding regions of duplicated genes, often in transcriptional regulatory regions. DNA changes in regulatory sequences can influence any or all aspects of gene expression: the magnitude of expression, its developmental timing, induction by stimuli outside the cell including hormonal or metabolic signals, and the cell type in which expression is restricted.
  • the gene product of one paralog, gene A can complement the pathological loss or silencing of the other paralog, gene B, if expression of gene A is not limiting in the same cell.
  • Altering patterns of gene expression may offer profound therapeutic benefits for genetic conditions in which enhanced expression of a paralogous gene “rescues” a phenotype caused by a mutation in a paralog. This might be called autologous gene complementation.
  • a paralogous gene “rescues” a phenotype caused by a mutation in a paralog. This might be called autologous gene complementation.
  • ATP7B enhanced expression by pharmacologic induction of ATP7A, a closely related copper transporter protein, might rescue mutations in ATP7B, another copper transporter.
  • the basic function of each copper transporter protein has been preserved but following the duplication of the common ancestral gene, the expression of these two genes has been separated spatially, one confined to intestinal enterocytes, the other to hepatocytes. This is one of many examples of paralogous gene in which one gene can complement the loss of the second if appropriately expressed in the same cell or tissue.
  • a notable example of a paralogous gene family is the well-studied alpha and beta family of globin genes coding for the alpha and beta subunits of hemoglobin.
  • Five beta-like genes each arising by gene duplication are arrayed next to each other on chromosome 16 with each gene being transcribed in a temporally-specific manner throughout the 9 months of human embryonic and fetal development.
  • the five beta-like globin proteins share a high degree of protein sequence similarity, so much so that genetic mutations inactivating the adult beta globin gene can be clinically silent if expression of any one of the other 4 subunit members of the beta-like globin family is adequate.
  • Activation of expression and subsequent transcriptional silencing of each specific embryonic and fetal beta-like globin gene is regulated in part by epigenetic mechanisms.
  • the rescue of mutations in the beta globin gene, mutations which are responsible for diseases such as thalassemia major or sickle cell anemia, by transcriptional induction of one or more of the other beta-like genes through the pharmacologic manipulation of epigenetic silencing would be clinically beneficial.
  • Autologous activation with a pharmacologic agent of a functionally complementary paralog of a mutated or pathologically silenced gene may be a more successful therapeutic strategy than replacing or repairing the mutated gene with a wild-type (normal) copy.
  • KDM1A (also known as Lysine-Specific Demethylase 1 (LSD1) or AOF2 or BHC110) was the first enzyme with specific lysine demethylase activity to be described demonstrating unequivocally that histone modifications are reversible rather than permanent.
  • KDM1A is a histone H3 lysine demethylase that catalyzes the oxidative demethylation of H3K4me1 or me2 and H3K9me1 or me2 but not the substrate H3K4me3.
  • the enzyme also demethylates non-histone proteins such as p53 and Gfi1.
  • KDM1A contains an amine oxidase domain that demethylates H3Kme substrate in a flavin adenine dinucleotide (FAD)-dependent manner similar to other monoamine (MAO) and polyamine oxidase inhibitors. Indeed, non-specific inhibitors of MAO enzymes can inhibit the demethylase activity of KDM1A
  • KDM1A is over-expressed in many human cancers including Wilm's tumor, small-cell lung, bladder, prostate, breast, head & neck, colon, and ovarian cancer and associated with more frequent relapses.
  • KDM1A is required for transcriptional regulation mediated by the androgen receptor in prostate cancer, the estrogen receptor in breast carcinomas, and the TLX receptor in neuroblastoma. Knockdown of KDM1A expression decreases proliferation of cancer cells.
  • KDM1A is also overexpressed in cancer cells that are nuclear hormone receptor-independent including ER-negative breast. Potent, selective small molecule inhibitors of KDM1A should be useful for treatment of these and other cancers in which KDM1A activity is overabundant.
  • the structure and state of chromatin can also influence the ability of a pathogenic virus to insert into host DNA, undergo transcription and replicate.
  • Infection by the alpha herpes viruses herpes simplex virus (HSV) and varicella-zoster virus (VSV) effect the remodeling of chromatin after infection of host cells to counter the rapid deposition of nucleosomes containing histones with transcriptional repressive marks by employing virus-encoded transcription factors to recruit the host HCF-1 co-activator complex that contains KDM1A and the histone H3K4 methyltransferases Set1 or MLL family members.
  • HSV herpes simplex virus
  • VSV varicella-zoster virus
  • KDM1A activity has on the transcription of specific genes is dependent on recruitment of KDM1A to a specific gene promoter region via DNA binding proteins.
  • proteins that bind KDM1A determine where along the chromosome the demethylase activity is targeted.
  • KDM1A KDM1A/CoREST complex which may also include DNMT1 and NuRD among other factors is particularly important for the repression of expression of specific genes.
  • KDM1A is recruited to the promoter region of genes through site-specific transcription factors.
  • factors include among others the androgen receptor, the estrogen receptor alpha, Snail1, Slug, HIV Tat, ZEB1, RBP-J, PIT1, REST, NR2C1, NR2C2 and isoforms of Gfi1b.
  • These transcription factors can recruit KDM1A to participate in activation of gene expression or silencing of gene expression depending on the cell type and the specific transcription factors.
  • Acetyl-coenzyme A, nicotinamide adenine dinucleotide (NAD) and alpha-ketoglutarate also influence histone methylation and acetylation states.
  • Flavin adenine dinucleotide is a required co-factor for KDM1A.
  • FAD in conjunction with NAD and NADP act as cellular redox sensors.
  • KDM1A temporarily converts FAD to FADH after which an electron acceptor, likely O 2 and others, completes the catalytic cycle by regenerating FAD and H 2 O 2 .
  • the cellular redox state influences KDM1A activity both by its ability to oxidize FADH and other electron acceptors.
  • chromatin states hence gene expression, can be altered by the variable concentrations of metabolic intermediates and in the specific case of KDM1A that activity is entirely dependent on FAD whose concentration fluctuates as a function of the energetic economy of the cell.
  • KDM1A can lower serum glucose, reduced hepatic glycogen, and is a powerful insulin secretagogue.
  • Pharmaceutical manipulation of KDM1A activity may thus prove useful for the treatment of diseases that represent pathological aberrations of the energy status of the cell including metabolic syndrome, dyslipidemias, diabetes, obesity, anorexia, failure to thrive, cachexia, lipodystrophies, and steatohepatitis.
  • the steroid hormones estradiol and testosterone and related compound play a key role in both normal development and in pathological states such as breast and prostate cancer in which tumor cell growth is dependent on hormonal signaling.
  • the biological effects of steroid hormones are mediated by structurally and functionally distinct ligand-binding receptors that function as a transcription factor recruited to a specific DNA binding site.
  • the ligand-bound steroid receptors act as the principal transcriptional regulator of hormone effects. Transcriptional activation of gene expression for all steroid-dependent hormones is dependent on chromatin structure and the presence of co-factors.
  • the estrogen receptor employs, for example, the co-factors SRC1, SRC2, AIB1, PELP1, CBP, p300, PCAF, CARM1, PRMT1 and co-repressors such as NCoR, SMRT and MTA1.
  • the transcriptional response to hormone stimulation is dependent on the interaction of these co-factors and repressors as well as the state of chromatin, especially modification of histones by histone-modifying enzymes associated with the co-regulators.
  • Both estrogenic and androgenic hormone stimulation induces several histone modifications at the promoters of target genes that alter the acetylation, phosphorylation and methylation state of local histones.
  • KDM1A activity is required to affect the maximal rate of transcription for a hormone-responsive gene.
  • KDMA1 should prove useful as a therapeutic target of pharmaceuticals in blunting or ablating the hormone-dependence of tumor cells.
  • This same therapeutic logic applies to other ligand-dependent transcription factors whose transcriptional activation is partly or wholly dependent on KDM1A activity to alter chromatin states sufficiently to facilitate transcription—examples of these would include the vitamin D, retinoid and lipid-activated receptors.
  • These agents include 5′-azacytidine and 5′-aza-2′ deoxycytidine (decitabine) which inhibit DNMT1 or other DNA methyltransferases known to be present and active at promoter sites of silenced genes such as gamma globin promoter; vorinostat and panobinostat or other inhibitors of histone deacetylase (HDAC) enzymes; hydroxyurea (HU), valproate and sodium butyrate and its analogues each of which may interfere with the activity of orphan nuclear receptors. All of these agents enjoy some clinical use principally in the management of neoplastic disease. Though some clinical utility of these agents for other disease states has been demonstrated, these agents have not been widely adopted because of their modest therapeutic effects and their toxicity.
  • decitabine 5′-azacytidine and 5′-aza-2′ deoxycytidine (decitabine) which inhibit DNMT1 or other DNA methyltransferases known to be present and active at promoter sites of silenced genes such as gam
  • HbF hemoglobin F
  • Such targets include any of the interfaces of the specific protein-protein contacts, for example, the NuRD complex and KDM1A; the DNA binding recognition domains of, for example, NR2C1 and NR2C2; the ligand binding domains of, for example, NR2C1 and NR2C2; the enzyme activities such as lysine demethylase, for example, KDM1A; histone deacetylases (HDAC), for example HDAC1, 2, or 3; DNA methyltransferases, for example, DNMT1.
  • the enzyme activities such as lysine demethylase, for example, KDM1A; histone deacetylases (HDAC), for example HDAC1, 2, or 3; DNA methyltransferases, for example, DNMT1.
  • compositions and methods for altering gene expression in cells and tissues sufficient to restore the cell or tissue to normal physiologic function including, e.g., appropriate apoptosis in the case of cancer, or to alter the pathological phenotype of the cell, tissue, organ or organism by inducing the expression of one or more genes sufficiently to suppress the pathological state.
  • FIG. 1 shows an XRPD diffractogram of amorphous Example 1 bis-tosylate.
  • FIG. 2 shows XRPD diffractograms of Example 1 bis-tosylate Form 2; the upper was recrystallized from semicrystalline solid.
  • FIG. 3 shows the 1H NMR spectrum of Example 1 bis-tosylate Form 2 recrystallized from semicrystalline solid.
  • FIG. 4 shows the DCS and TGA of Example 1 bis-tosylate Form 2 recrystallized from semicrystalline solid.
  • FIG. 5 shows XRPD diffractograms of Example 1 bis-tosylate Form 2; the upper was synthesized in ACN.
  • FIG. 6 shows the 1H NMR spectrum of Example 1 bis-tosylate Form 2 synthesized in ACN.
  • FIG. 7 shows the DCS and TGA of Example 1 bis-tosylate Form 2 synthesized in ACN.
  • FIG. 8 shows XRPD diffractograms of Example 1 bis-tosylate forms 2 (A), 3 (E), 4 (D), and 5 (B and C, from high-resolution and high-throughput scans, respectively); extra peaks compared to Form 2, noted with dashed lines, prompted additional characterization of Forms 3, 4, and 5.
  • FIG. 9 shows XRPD diffractograms of Example 1 bis-tosylate form 2 and semicrystalline form 3 from tetrahydrofuran (F) and toluene (G); extra peaks compared to Form 2, noted with dashed lines, prompted additional characterization.
  • FIG. 10 shows XRPD diffractograms of solid material recovered in salt experiments in various solvents.
  • A is a weakly crystalline sulfate;
  • B is amorphous phosphate;
  • C is amorphous tartrate;
  • D is amorphous sulfate;
  • E is amorphous phosphate;
  • F is amorphous tartrate;
  • G is amorphous fumarate;
  • H is amorphous sulfate;
  • FIG. 11 shows XRPD diffractograms of solid material recovered in salt experiments in various solvents after maturation.
  • A is amorphous hydrochloride from MTBE;
  • B is partially crystalline sulfate pattern 1;
  • C is amorphous mesylate from IPA;
  • D is partially crystalline phosphate pattern 1;
  • E is amorphous tartrate;
  • F is amorphous fumarate;
  • G is amorphous sulfate;
  • H is amorphous mesylate from MTBE;
  • M is amorphous mesylate from MTBE;
  • N is amorphous phosphate;
  • O is amorphous tartrate; and
  • P is weakly crystalline fumarate pattern 1.
  • FIG. 12 shows XRPD diffractograms of solid material recovered in salt experiments in methylethyl ketone.
  • A is amorphous sulfate;
  • B is amorphous oxalate;
  • C is galactaric acid;
  • D is amorphous tartrate;
  • E is amorphous sulfate;
  • F is p-TSA (tosylate) Form 1;
  • G is amorphous oxalate;
  • H is galactaric acid; I is weakly crystalline ascorbate; J is amorphous tartrate.
  • FIG. 13 shows XRPD diffractograms of solid material recovered in salt experiments in methylethyl ketone after maturation.
  • A is the sulfate pattern 2;
  • B is the oxalate Form 1;
  • C is galactaric acid;
  • D is amorphous tartrate;
  • E is galactaric acid; and
  • F is weakly crystalline tartrate.
  • FIG. 14 shows XRPD diffractograms of solid material recovered in salt experiments in MeCN.
  • A is weakly crystalline sulfate; B is weakly crystalline oxalate; C is galactaric acid; D is amorphous sulfate; E is tosylate Form 2; F is amorphous oxalate; G is galactaric acid; H is amorphous tartrate.
  • FIG. 15 shows XRPD diffractograms of solid material recovered in salt experiments in MeCN after maturation.
  • A is sulfate pattern 3;
  • B is oxalate form 1;
  • C is galactaric acid;
  • D is amorphous tartrate;
  • E is amorphous oxalate;
  • F is galactaric acid;
  • G is amorphous tartrate.
  • FIG. 16 is a high-resolution XRPD diffractogram of the tartrate form 2 salt.
  • FIG. 17 is a high-resolution XRPD diffractogram of the oxalate form 1 salt.
  • FIG. 18 is a high-resolution XRPD diffractogram of the tartrate form 1 salt.
  • FIG. 19 is a high-resolution XRPD diffractogram of the tartrate form 3 salt.
  • FIG. 20 is a high-resolution XRPD diffractogram of the oxalate form 2 salt.
  • FIG. 21 shows XRPD diffractograms of sulfate salt forms from the second salt experiment.
  • FIG. 22 shows XRPD diffractograms of benzenesulfonate salt forms from the second salt experiment.
  • FIG. 23 shows XRPD diffractograms of oxalate salt forms from the second salt experiment.
  • FIG. 24 is an XRPD diffractogram of fumarate salt forms from the second salt experiment.
  • FIG. 25 is an XRPD diffractogram of the besylate salt from the second salt experiment.
  • FIG. 26 is an XRPD diffractogram of L-malate salt from the second salt experiment.
  • FIG. 27 is an XRPD diffractogram of L-malate salt from the second salt experiment.
  • Y is chosen from a bond, NR 4a , O, C(O)NH, NHC(O), S, SO 2 , CHOH, and CH 2 ;
  • Z is chosen from a bond, NR 4b , O, C(O)NH, NHC(O), S, SO 2 , and CH 2 ;
  • n is chosen from 0, 1, 2, 3, 4, and 5;
  • n is chosen from 0, 1, 2, and 3;
  • R 1 and R 2 are each independently chosen from alkyl, aminoalkyl, alkylsulfonylalkyl, alkoxyalkyl, aryl, arylalkyl, cycloalkyl, cycloalkylalkyl, phenyl, biphenyl, heteroaryl, heteroarylalkyl, heterocycloalkyl, and heterocycloalkylalkyl and R 1 and R 2 , together with the nitrogen to which they attach, form a nitrogen-containing heterocycloalkyl or heteroaryl ring, which may be optionally substituted with between 0 and 3 R 6 groups;
  • R 3 is chosen from alkylamino, cycloalkylamino, arylamino, heteroarylamino, heterocycloalkylamino, cycloalkyl, cycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, heterocycloalkyl, and heterocycloalkylalkyl any of which may be optionally substituted with between 0 and 3 R 6 groups;
  • R 4 , R 4a , and R 4b are independently chosen from hydrogen, alkyl, alkenyl, alkynyl, and cycloalkyl;
  • R 5 is chosen from aryl and heteroaryl, any of which may be optionally substituted with between 0 and 3 R 6 groups;
  • each R 6 is independently chosen from hydrogen, halogen, alkyl, alkylsulfonylaryl, alkenyl, alkynyl, cycloalkyl, haloalkyl, haloalkoxy, haloaryl, alkoxyaryl, aryl, aryloxy, aralkyl, heterocycloalkyl, heteroaryl, alkylheteroaryl, heteroarylalkyl, cyano, alkoxy, alkoxyaryl, amino, alkylamino, dialkylamino, oxo, COR 7 , SO 2 R 7 , NHSO 2 R 7 , NHSO 2 NHR 7 , NHCOR 7 , NHCONHR 7 , CONHR 7 , and CONR 7 R 8 ; and
  • R 7 and R 8 are independently chosen from hydrogen, aryl, and lower alkyl; or R 7 and R 8 may be taken together to form a nitrogen-containing heterocycloalkyl or heteroaryl ring, which may be optionally substituted with lower alkyl.
  • the compound has Formula Ia, Ib, Ic, or Id:
  • the compound has Formula II or III:
  • the compound has Formula IIa, IIb, IIc, or IId:
  • Z is NR 4b .
  • R 4b is chosen from methyl and hydrogen.
  • R 4b is hydrogen
  • the alkyl is C 1 -C 8 alkyl.
  • R 3 is aryl, which may be optionally substituted with between 0 and 3 R 6 groups.
  • R 3 is chosen from aryl and heteroaryl, either of which is substituted with an R 6 group called R 6a , chosen from heteroaryl, cyano, and S(O) 2 N(CH 3 ) 2 . In certain embodiments, R 3 remains optionally substituted with 1-2 additional R 6 groups.
  • n is chosen from 0, 1, and 2.
  • n 2
  • R 3 is chosen from phenyl and heteroaryl, either of which is substituted with an R 6 group called R 6a , chosen from heteroaryl, cyano, and S(O) 2 N(CH 3 ) 2 .
  • R 6a is chosen from cyano, S(O) 2 N(CH 3 ) 2 ,
  • R 6a is heteroaryl
  • R 6a is chosen from:
  • R 6a is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • R 4 is hydrogen
  • nitrogen-containing heterocycloalkyl or heteroaryl ring formed by R 1 and R 2 together with the nitrogen to which they are attached contains 3 to eight atoms.
  • R 1 and R 2 are taken together to form a nitrogen-containing heterocycloalkyl, which may be optionally substituted with between 0 and 3 R 6 groups.
  • the nitrogen-containing heterocycloalkyl is chosen from:
  • the nitrogen-containing heterocycloalkyl is chosen from:
  • the nitrogen-containing heterocycloalkyl is:
  • the nitrogen-containing heterocycloalkyl is optionally substituted with between 0 and 3 R 6 groups chosen from alkyl and oxo.
  • R 5 is phenyl, which may be optionally substituted with between 0 and 3 R 6 groups.
  • R 5 is:
  • R 6b is chosen from halogen and hydroxy.
  • R 6b is chosen from fluoro, methoxy, and hydroxy.
  • R 6b is fluoro
  • R 4b is chosen from methyl and hydrogen.
  • R 4b is hydrogen
  • the compound has Formula IV:
  • Y is chosen from a bond, NR 4a , O, C(O)NH, NHC(O), S, SO 2 , CHOH, and CH 2 ;
  • Z is chosen from a bond, NR 4b , O, C(O)NH, NHC(O), S, SO 2 , and CH 2 ;
  • n is chosen from 0, 1, 2, 3, 4, and 5;
  • n is chosen from 0, 1, 2, and 3;
  • R 1 and R 2 are each independently chosen from alkyl, aminoalkyl, alkylsulfonylalkyl, alkoxyalkyl, aryl, arylalkyl, cycloalkyl, cycloalkylalkyl, phenyl, biphenyl, heteroaryl, heteroarylalkyl, heterocycloalkyl, and heterocycloalkylalkyl and R 1 and R 2 , together with the nitrogen to which they attach, form a nitrogen-containing heterocycloalkyl or heteroaryl ring, which may be optionally substituted with between 0 and 3 R 6 groups;
  • R 3 is chosen from alkylamino, cycloalkylamino, arylamino, heteroarylamino, heterocycloalkylamino, cycloalkyl, cycloalkylalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, heterocycloalkyl, and heterocycloalkylalkyl any of which may be optionally substituted with between 0 and 3 R 6 groups;
  • R 4a and R 4b are independently chosen from hydrogen, alkyl, alkenyl, alkynyl, and cycloalkyl;
  • R 5 is chosen from aryl and heteroaryl, any of which may be optionally substituted with between 0 and 3 R 6 groups;
  • R 6a is chosen from heteroaryl, cyano, and S(O) 2 N(CH 3 ) 2 ;
  • each R 6 is independently chosen from hydrogen, halogen, alkyl, alkylsulfonylaryl, alkenyl, alkynyl, cycloalkyl, haloalkyl, haloalkoxy, haloaryl, alkoxyaryl, aryl, aryloxy, aralkyl, heterocycloalkyl, heteroaryl, alkylheteroaryl, heteroarylalkyl, cyano, alkoxy, alkoxyaryl, amino, alkylamino, dialkylamino, oxo, COR 7 , SO 2 R 7 , NHSO 2 R 7 , NHSO 2 NHR 7 , NHCOR 7 , NHCONHR 7 , CONHR 7 , and CONR 7 R 8 ; and
  • R 7 and R 8 are independently chosen from hydrogen, aryl, and lower alkyl; or R 7 and R 8 may be taken together to form a nitrogen-containing heterocycloalkyl or heteroaryl ring, which may be optionally substituted with lower alkyl.
  • Z is NR 4b .
  • R 4b is chosen from methyl and hydrogen.
  • R 4b is hydrogen
  • the alkyl is C 1 -C 8 alkyl.
  • n is chosen from 0, 1, and 2.
  • n is 2.
  • R 1 and R 2 are each independently chosen from alkyl, aminoalkyl, alkylsulfonylalkyl, alkoxyalkyl, and heteroaryl, and R 1 and R 2 , together with the nitrogen to which they attach, form a nitrogen-containing heterocycloalkyl or heteroaryl ring, which may be optionally substituted with between 0 and 3 R 6 groups.
  • the nitrogen-containing heterocycloalkyl or heteroaryl ring formed by R 1 and R 2 together with the nitrogen to which they are attached contains 3 to eight atoms.
  • R 1 and R 2 are taken together to form a nitrogen-containing heterocycloalkyl, which may be optionally substituted with between 0 and 3 R 6 groups.
  • the nitrogen-containing heterocycloalkyl is optionally substituted with between 0 and 3 R 6 groups chosen from alkyl, alkoxy, alkoxyalkyl, halogen, haloalkyl, haloalkoxy, hydroxy, hydroxyalkyl, alkylsulfonyl, alkylsulfonylalkyl, deuterium, trideuteromethyl, amino, —COOH, —CONH 2 , —SO 2 CH 3 , cyano, spiro-heterocycloalkyl, heteroaryl, and oxo.
  • R 6 groups chosen from alkyl, alkoxy, alkoxyalkyl, halogen, haloalkyl, haloalkoxy, hydroxy, hydroxyalkyl, alkylsulfonyl, alkylsulfonylalkyl, deuterium, trideuteromethyl, amino, —COOH, —CONH 2 , —SO 2 CH 3
  • the nitrogen-containing heterocycloalkyl is optionally substituted with between 0 and 3 R 6 groups chosen from alkyl, halogen, CONH 2 , SO 2 CH 3 , cyano, spiro-heterocycloalkyl, and oxo.
  • the nitrogen-containing heterocycloalkyl is chosen from:
  • the nitrogen-containing heterocycloalkyl is chosen from:
  • the nitrogen-containing heterocycloalkyl is:
  • R 6a is heteroaryl
  • R 6a is chosen from cyano, S(O) 2 N(CH 3 ) 2 ,
  • R 6a is chosen from
  • R 5 is phenyl, which may be optionally substituted with between 0 and 3 R 6 groups.
  • R 5 is:
  • R 6b is chosen from halogen, hydroxy, and methoxy.
  • R 6b is chosen from fluoro, methoxy, and hydroxy.
  • R 6b is fluoro
  • the compound has Formula V:
  • R 1 and R 2 are each independently chosen from alkyl, aminoalkyl, alkylsulfonylalkyl, alkoxyalkyl, aryl, arylalkyl, cycloalkyl, cycloalkylalkyl, phenyl, biphenyl, heteroaryl, heteroarylalkyl, heterocycloalkyl, and heterocycloalkylalkyl and R 1 and R 2 , together with the nitrogen to which they attach, form a nitrogen-containing heterocycloalkyl or heteroaryl ring, which may be optionally substituted with between 0 and 3 R 6 groups;
  • R 4b is chosen from hydrogen, alkyl, alkenyl, alkynyl, and cycloalkyl
  • R 6a is chosen from heteroaryl, cyano, and S(O) 2 N(CH 3 ) 2 ;
  • each R 6 and each R 6b is independently chosen from hydrogen, halogen, alkyl, alkylsulfonylaryl, alkenyl, alkynyl, cycloalkyl, haloalkyl, haloalkoxy, haloaryl, alkoxyaryl, aryl, aryloxy, aralkyl, heterocycloalkyl, heteroaryl, alkylheteroaryl, heteroarylalkyl, cyano, alkoxy, alkoxyaryl, amino, alkylamino, dialkylamino, oxo, COR 7 , SO 2 R 7 , NHSO 2 R 7 , NHSO 2 NHR 7 , NHCOR 7 , NHCONHR 7 , CONHR 7 , and CONR 7 R 8 ; and
  • R 7 and R 8 are independently chosen from hydrogen, aryl, and lower alkyl; or R 7 and R 8 may be taken together to form a nitrogen-containing heterocycloalkyl or heteroaryl ring, which may be optionally substituted with lower alkyl.
  • R 4b is chosen from methyl and hydrogen.
  • R 4b is hydrogen
  • R 6a is chosen from cyano, S(O) 2 N(CH 3 ) 2 ,
  • R 1 and R 2 are each independently chosen from alkyl, aminoalkyl, alkylsulfonylalkyl, alkoxyalkyl, and heteroaryl, and R 1 and R 2 , together with the nitrogen to which they attach, form a nitrogen-containing heterocycloalkyl or heteroaryl ring, which may be optionally substituted with between 0 and 3 R 6 groups
  • the nitrogen-containing heterocycloalkyl or heteroaryl ring formed by R 1 and R 2 together with the nitrogen to which they are attached contains 3 to eight atoms.
  • R 1 and R 2 are taken together to form a nitrogen-containing heterocycloalkyl, which may be optionally substituted with between 0 and 3 R 6 groups.
  • the nitrogen-containing heterocycloalkyl is chosen from:
  • the nitrogen-containing heterocycloalkyl is chosen from:
  • the nitrogen-containing heterocycloalkyl is:
  • R 6b is chosen from fluoro, methoxy, and hydroxy.
  • R 6b is fluoro
  • any embodiment above may be combined with any one or more of these embodiments, provided the combination is not mutually exclusive.
  • two embodiments are “mutually exclusive” when one is defined to be something which cannot overlap with the other.
  • Y is CH 2
  • Y is NR 4b
  • R 1 and R 2 are taken together to form a nitrogen-containing heterocycloalkyl
  • R 5 is phenyl optionally substituted with fluorine.
  • the compound is chosen from the Examples disclosed herein, or a salt, polymorph, or solvate thereof. In certain embodiments, the compound is chosen from the Examples disclosed herein, or a salt, polymorph, or solvate thereof, wherein R 6a is chosen from heteroaryl, cyano, and S(O) 2 N(CH 3 ) 2 . In certain embodiments, the compound is chosen from the Examples disclosed herein, or a salt, polymorph, or solvate thereof, wherein R 6a is chosen from heteroaryl and cyano. In certain embodiments, the compound is chosen from the Examples disclosed herein, or a salt, polymorph, or solvate thereof, wherein R 6a is heteroaryl.
  • salt of a compound as disclosed herein, or a polymorph or solvate thereof is also provided herein.
  • the salt has Formula VI:
  • X is chosen from tosylate, sulfate, tartrate, oxalate, besylate, fumarate, citric, esylate, and malate;
  • q is an integer chosen from 1 and 2.
  • X is tosylate.
  • q is 2.
  • a tosylate salt of a compound as disclosed herein, or a polymorph or solvate thereof is also provided herein.
  • a bis-tosylate salt of a compound as disclosed herein, or a polymorph or solvate thereof is also provided herein.
  • a compound, or a salt, polymorph, or solvate thereof, as disclosed herein is provided for use as a medicament. Also provided herein is a compound as disclosed herein, or a salt, polymorph, or solvate thereof, for use in the manufacture of a medicament for the prevention or treatment of a KDM1A-mediated disease.
  • a compound as disclosed herein is for use in the manufacture of a medicament for the prevention or treatment of a disease or condition chosen from sickle cell disease, thalassemia major, and other beta-hemoglobinopathies.
  • composition which comprises a compound as disclosed herein, together with a pharmaceutically acceptable carrier.
  • the pharmaceutical composition is formulated for oral administration.
  • the pharmaceutical composition additionally comprises another therapeutic agent.
  • Also provided herein is a method of inhibiting KDM1A is provided, comprising contacting KDM1A with a compound as disclosed herein.
  • Also provided herein is a method of treatment of a KDM1A-mediated disease comprising the administration of a therapeutically effective amount of a compound as disclosed herein, or a salt, polymorph, or solvate thereof, to a patient in need thereof.
  • the disease is cancer.
  • the cancer is chosen from Ewing's sarcoma, multiple myeloma, T-cell leukemia, Wilm's tumor, small-cell lung cancer, bladder cancer, prostate cancer, breast cancer, head/neck cancer, colon cancer, and ovarian cancer.
  • the disease is a myeloid disease.
  • the myeloid disease is chosen from myelofibrosis, polycythemia vera, essential thrombocythemia, myelodysplastic syndrome (MDS), acute myelogenous leukemia (AML), and chronic myelogenous leukemia (CML).
  • myelofibrosis myelofibrosis, polycythemia vera, essential thrombocythemia, myelodysplastic syndrome (MDS), acute myelogenous leukemia (AML), and chronic myelogenous leukemia (CML).
  • the disease is an inflammatory disease.
  • the inflammatory disease is chosen from inflammatory bowel disease, rheumatoid arthritis, or systemic lupus erythematosus.
  • Also provided herein is a method of treatment of a globin-mediated disease comprising the administration of a therapeutically effective amount of a compound as disclosed herein, or a salt, polymorph, or solvate thereof, to a patient in need thereof.
  • a method for achieving an effect in a patient comprising the administration of a therapeutically effective amount of a compound as disclosed herein; wherein the effect is chosen from an elevation of red blood cell count, an elevation of the red blood cell count of red cells containing fetal hemoglobin, an elevation in the total concentration of fetal hemoglobin in red cells, an elevation in the total concentration of fetal hemoglobin in reticulocytes, an increase in the transcription of the gamma globin gene in bone marrow-derived red cell precursors, e.g., pro-erythroblasts, a reduction in the number of sickle cell crises a patient experiences over a unit period of time, a halt to or prevention of tissue damage e.g.
  • Also provided herein is a method of inhibiting at least one KDM1A function comprising the step of contacting KDM1A with a compound as disclosed herein; wherein the inhibition is measured by phenotype of red cells or their precursors either cultured or in vivo in humans or mouse or transgenic mice containing the human beta globin locus or portions thereof, the ability of cancer cells to proliferate, the expression of specific genes known to be regulated by KDM1A activity such as gamma globin, a change in the histone methylation states, a change in the methylation state of proteins known to be demethylated by KDM1A such as G9a or SUV39H1, expression of KDM1A-regulated genes, or binding of KDM1A with a natural binding partner such as CoREST, DNMT1 or HDACs.
  • a natural binding partner such as CoREST, DNMT1 or HDACs.
  • KDM1A KDM1A
  • combination therapies are often additive or synergistic in their therapeutic effects and may even be necessary to achieve the full clinical benefit desired.
  • ATRA all-trans retinoic acid
  • arsenic trioxide arsenic trioxide
  • inhibitors of DNA methyltransferases such as 5′-azacytidine or 5′-aza 2′-deoxycytidine
  • inhibitors of NF ⁇ B signaling such as sulindac or conventional anti-neoplastic agents such as anthracyclines or nucleoside analogues such as cytosine arabinoside.
  • agents that induce leukemia stem cells into the cell cycle may be useful as part of a combination including an LSD1 inhibitor.
  • any one of the listed items can be employed by itself or in combination with any one or more of the listed items.
  • the expression “A and/or B” is intended to mean either or both of A and B, i.e. A alone, B alone or A and B in combination.
  • the expression “A, B and/or C” is intended to mean A alone, B alone, C alone, A and B in combination, A and C in combination, B and C in combination or A, B, and C in combination.
  • a “therapeutically effective amount” of a drug is an amount of drug or its pharmaceutically acceptable salt that eliminates, alleviates, or provides relief of the symptoms of the disease for which it is administered.
  • a “subject in need thereof” is a human or non-human animal that exhibits one or more symptoms or indicia of a disease.
  • n is set at 0 in the context of “0 carbon atoms”, it is intended to indicate a bond or null.
  • alkylsulfonyl as used herein, means an alkyl group, as defined herein, appended to the parent molecular moiety through a sulfonyl group, as defined herein.
  • Representative examples of alkylsulfonyl include, but are not limited to, methylsulfonyl and ethylsulfonyl.
  • alkylsulfonylalkyl as used herein, means an alkylsulfonyl group, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein.
  • Representative examples of alkylsulfonylalkyl include, but are not limited to, methylsulfonylmethyl and ethylsulfonylmethyl.
  • acyl refers to a carbonyl attached to an alkenyl, alkyl, aryl, cycloalkyl, heteroaryl, heterocycle, or any other moiety where the atom attached to the carbonyl is carbon.
  • An “acetyl” group refers to a —C(O)CH 3 group.
  • An “alkylcarbonyl” or “alkanoyl” group refers to an alkyl group attached to the parent molecular moiety through a carbonyl group. Examples of such groups include methylcarbonyl and ethylcarbonyl. Examples of acyl groups include formyl, alkanoyl and aroyl.
  • alkenyl refers to a straight-chain or branched-chain hydrocarbon group having one or more double bonds and containing from 2 to 20 carbon atoms. In certain embodiments, said alkenyl will comprise from 2 to 6 carbon atoms.
  • alkenylene refers to a carbon-carbon double bond system attached at two or more positions such as ethenylene [(—CH ⁇ CH—), (—C::C—)]. Examples of suitable alkenyl groups include ethenyl, propenyl, 2-methylpropenyl, 1,4-butadienyl and the like. Unless otherwise specified, the term “alkenyl” may include “alkenylene” groups.
  • alkoxy refers to an alkyl ether group, wherein the term alkyl is as defined below.
  • suitable alkyl ether groups include methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, iso-butoxy, sec-butoxy, tert-butoxy, and the like.
  • alkyl refers to a straight-chain or branched-chain alkyl group containing from 1 to 20 carbon atoms. In certain embodiments, said alkyl will comprise from 1 to 10 carbon atoms. In further embodiments, said alkyl will comprise from 1 to 6 carbon atoms. Alkyl groups may be optionally substituted as defined herein. Examples of alkyl groups include methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, pentyl, iso-amyl, hexyl, octyl, noyl and the like.
  • alkylene refers to a saturated aliphatic group derived from a straight or branched chain saturated hydrocarbon attached at two or more positions, such as methylene (—CH 2 —). Unless otherwise specified, the term “alkyl” may include “alkylene” groups.
  • alkylamino refers to an alkyl group attached to the parent molecular moiety through an amino group. Suitable alkylamino groups may be mono- or dialkylated, forming groups such as, for example, N-methylamino, N-ethylamino, N,N-dimethylamino, N,N-ethylmethylamino and the like.
  • alkylidene refers to an alkenyl group in which one carbon atom of the carbon-carbon double bond belongs to the moiety to which the alkenyl group is attached.
  • alkylthio refers to an alkyl thioether (R—S—) group wherein the term alkyl is as defined above and wherein the sulfur may be singly or doubly oxidized.
  • suitable alkyl thioether groups include methylthio, ethylthio, n-propylthio, isopropylthio, n-butylthio, iso-butylthio, sec-butylthio, tert-butylthio, methanesulfonyl, ethanesulfinyl, and the like.
  • alkynyl refers to a straight-chain or branched-chain hydrocarbon group having one or more triple bonds and containing from 2 to 20 carbon atoms. In certain embodiments, said alkynyl comprises from 2 to 6 carbon atoms. In further embodiments, said alkynyl comprises from 2 to 4 carbon atoms.
  • alkynylene refers to a carbon-carbon triple bond attached at two positions such as ethynylene (—C ⁇ C—).
  • alkynyl groups include ethynyl, propynyl, hydroxypropynyl, butyn-1-yl, butyn-2-yl, pentyn-1-yl, 3-methylbutyn-1-yl, hexyn-2-yl, and the like.
  • alkynyl may include “alkynylene” groups.
  • acylamino as used herein, alone or in combination, embraces an acyl group attached to the parent moiety through an amino group.
  • An example of an “acylamino” group is acetylamino (CH 3 C(O)NH—).
  • amino refers to —NRR′, wherein R and R′ are independently chosen from hydrogen, alkyl, hydroxyalkyl, acyl, heteroalkyl, aryl, cycloalkyl, heteroaryl, and heterocycloalkyl, any of which may themselves be optionally substituted. Additionally, R and R′ may combine to form heterocycloalkyl, either of which may be optionally substituted.
  • amino acid refers to a —NHCHRC(O)O— group, which may be attached to the parent molecular moiety to give either an N-terminus or C-terminus amino acid, wherein R is independently chosen from hydrogen, alkyl, aryl, heteroaryl, heterocycloalkyl, aminoalkyl, amido, amidoalkyl, carboxyl, carboxylalkyl, guanidinealkyl, hydroxyl, thiol, and thioalkyl, any of which themselves may be optionally substituted.
  • C-terminus refers to the parent molecular moiety being bound to the amino acid at the amino group, to give an amide as described herein, with the carboxyl group unbound, resulting in a terminal carboxyl group, or the corresponding carboxylate anion.
  • N-terminus refers to the parent molecular moiety being bound to the amino acid at the carboxyl group, to give an ester as described herein, with the amino group unbound resulting in a terminal secondary amine, or the corresponding ammonium cation.
  • C-terminus refers to —NHCHRC(O)OH or to —NHCHRC(O)O— and N-terminus refers to H 2 NCHRC(O)O— or to H 3 N + CHRC(O)O—.
  • aminoalkyl refers to an amino group as defined herein linked through an alkyl group to the parent moiety.
  • aryl as used herein, alone or in combination, means a carbocyclic aromatic system containing one, two or three rings wherein such polycyclic ring systems are fused together.
  • aryl embraces aromatic groups such as phenyl, naphthyl, anthracenyl, and phenanthryl.
  • arylalkenyl or “aralkenyl,” as used herein, alone or in combination, refers to an aryl group attached to the parent molecular moiety through an alkenyl group.
  • arylalkoxy or “aralkoxy,” as used herein, alone or in combination, refers to an aryl group attached to the parent molecular moiety through an alkoxy group.
  • arylalkyl or “aralkyl,” as used herein, alone or in combination, refers to an aryl group attached to the parent molecular moiety through an alkyl group.
  • arylalkynyl or “aralkynyl,” as used herein, alone or in combination, refers to an aryl group attached to the parent molecular moiety through an alkynyl group.
  • arylalkanoyl or “aralkanoyl” or “aroyl,” as used herein, alone or in combination, refers to an acyl group derived from an aryl-substituted alkanecarboxylic acid such as benzoyl, naphthoyl, phenylacetyl, 3-phenylpropionyl (hydrocinnamoyl), 4-phenylbutyryl, (2-naphthyl)acetyl, 4-chlorohydrocinnamoyl, and the like.
  • an aryl-substituted alkanecarboxylic acid such as benzoyl, naphthoyl, phenylacetyl, 3-phenylpropionyl (hydrocinnamoyl), 4-phenylbutyryl, (2-naphthyl)acetyl, 4-chlorohydrocinnamoyl, and the like.
  • aryloxy refers to an aryl group attached to the parent molecular moiety through an oxy.
  • biphenyl refers to two phenyl groups connected at one carbon site on each ring.
  • carbamate refers to an ester of carbamic acid (—NHCOO—) which may be attached to the parent molecular moiety from either the nitrogen or acid end, and which may be optionally substituted as defined herein.
  • O-carbamyl as used herein, alone or in combination, refers to a —OC(O)NRR′ group, with R and R′ as defined herein.
  • N-carbamyl as used herein, alone or in combination, refers to a ROC(O)NR′— group, with R and R′ as defined herein.
  • carbonyl when alone includes formyl [—C(O)H] and in combination is a —C(O)— group.
  • carboxyl or “carboxy,” as used herein, refers to —C(O)OH or the corresponding “carboxylate” anion, such as is in a carboxylic acid salt.
  • An “O-carboxy” group refers to a RC(O)O— group, where R is as defined herein.
  • a “C-carboxy” group refers to a —C(O)OR groups where R is as defined herein.
  • cyano as used herein, alone or in combination, refers to —CN.
  • cycloalkyl or, alternatively, “carbocycle,” as used herein, alone or in combination, refers to a saturated or partially saturated monocyclic, bicyclic or tricyclic alkyl group wherein each cyclic moiety contains from 3 to 12 carbon atom ring members and which may optionally be a benzo fused ring system which is optionally substituted as defined herein.
  • said cycloalkyl will comprise from 5 to 7 carbon atoms.
  • cycloalkyl groups examples include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, tetrahydronaphthyl, indanyl, octahydronaphthyl, 2,3-dihydro-1H-indenyl, adamantyl and the like.
  • “Bicyclic” and “tricyclic” as used herein are intended to include both fused ring systems, such as decahydronaphthalene, octahydronaphthalene as well as the multicyclic (multicentered) saturated or partially unsaturated type. The latter type of isomer is exemplified in general by, bicyclo[1,1,1]pentane, camphor, adamantane, and bicyclo[3,2,1]octane.
  • esters refers to a carboxy group bridging two moieties linked at carbon atoms.
  • ether refers to an oxy group bridging two moieties linked at carbon atoms.
  • guanidine refers to —NHC( ⁇ NH)NH 2 , or the corresponding guanidinium cation.
  • halo or halogen, as used herein, alone or in combination, refers to fluorine, chlorine, bromine, or iodine.
  • haloalkoxy refers to a haloalkyl group attached to the parent molecular moiety through an oxygen atom.
  • haloalkyl refers to an alkyl group having the meaning as defined above wherein one or more hydrogen atoms are replaced with a halogen. Specifically embraced are monohaloalkyl, dihaloalkyl and polyhaloalkyl groups.
  • a monohaloalkyl group for one example, may have an iodo, bromo, chloro or fluoro atom within the group.
  • Dihalo and polyhaloalkyl groups may have two or more of the same halo atoms or a combination of different halo groups.
  • haloalkyl groups include fluoromethyl, difluoromethyl, trifluoromethyl, chloromethyl, dichloromethyl, trichloromethyl, pentafluoroethyl, heptafluoropropyl, difluorochloromethyl, dichlorofluoromethyl, difluoroethyl, difluoropropyl, dichloroethyl and dichloropropyl.
  • Haloalkylene refers to a haloalkyl group attached at two or more positions. Examples include fluoromethylene (—CFH—), difluoromethylene (—CF 2 —), chloromethylene (—CHCl—) and the like.
  • heteroalkyl refers to a stable straight or branched chain, or cyclic hydrocarbon group, or combinations thereof, fully saturated or containing from 1 to 3 degrees of unsaturation, consisting of the stated number of carbon atoms and from one to three heteroatoms chosen from O, N, and S, and wherein the nitrogen and sulfur atoms may optionally be oxidized and the nitrogen heteroatom may optionally be quaternized.
  • the heteroatom(s) O, N and S may be placed at any interior position of the heteroalkyl group. Up to two heteroatoms may be consecutive, such as, for example, —CH 2 —NH—OCH 3 .
  • heteroaryl refers to a 3 to 7 membered unsaturated heteromonocyclic ring, or a fused monocyclic, bicyclic, or tricyclic ring system in which at least one of the fused rings is aromatic, which contains at least one atom chosen from O, S, and N. In certain embodiments, said heteroaryl will comprise from 5 to 7 carbon atoms.
  • the term also embraces fused polycyclic groups wherein heterocyclic rings are fused with aryl rings, wherein heteroaryl rings are fused with other heteroaryl rings, wherein heteroaryl rings are fused with heterocycloalkyl rings, or wherein heteroaryl rings are fused with cycloalkyl rings.
  • heteroaryl groups include pyrrolyl, pyrrolinyl, imidazolyl, pyrazolyl, pyridyl, pyrimidinyl, pyrazinyl, pyridazinyl, triazolyl, pyranyl, furanyl, thienyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, thiadiazolyl, isothiazolyl, indolyl, isoindolyl, indolizinyl, benzimidazolyl, quinolyl, isoquinolyl, quinoxalinyl, quinazolinyl, indazolyl, benzotriazolyl, benzodioxolyl, benzopyranyl, benzoxazolyl, benzoxadiazolyl, benzothiazolyl, benzothiadiazolyl, benzofuranyl, benzothienyl, chromonyl
  • Exemplary tricyclic heterocyclic groups include carbazolyl, benzidolyl, phenanthrolinyl, dibenzofuranyl, acridinyl, phenanthridinyl, xanthenyl and the like.
  • heteroarylalkyl as used herein alone or as part of another group refers to alkyl groups as defined above having a heteroaryl substituent.
  • heterocycloalkyl and, interchangeably, “heterocycle,” as used herein, alone or in combination, each refer to a saturated, partially unsaturated, or fully unsaturated monocyclic, bicyclic, or tricyclic heterocyclic group containing at least one heteroatom as a ring member, wherein each said heteroatom may be independently chosen from nitrogen, oxygen, and sulfur.
  • said heterocycloalkyl will comprise from 1 to 4 heteroatoms as ring members.
  • said heterocycloalkyl will comprise from 1 to 2 heteroatoms as ring members.
  • said heterocycloalkyl will comprise from 3 to 8 ring members in each ring.
  • heterocycloalkyl will comprise from 3 to 7 ring members in each ring. In yet further embodiments, said heterocycloalkyl will comprise from 5 to 6 ring members in each ring.
  • “Heterocycloalkyl” and “heterocycle” are intended to include sulfones, sulfoxides, N-oxides of tertiary nitrogen ring members, and carbocyclic fused and benzo fused ring systems; additionally, both terms also include systems where a heterocycle ring is fused to an aryl group, as defined herein, or an additional heterocycle group.
  • heterocycle groups include aziridinyl, azetidinyl, 1,3-benzodioxolyl, dihydroisoindolyl, dihydroisoquinolinyl, dihydrocinnolinyl, dihydrobenzodioxinyl, dihydro[1,3]oxazolo[4,5-b]pyridinyl, benzothiazolyl, dihydroindolyl, dihy-dropyridinyl, 1,3-dioxanyl, 1,4-dioxanyl, 1,3-dioxolanyl, imidazolidinyl, isoindolinyl, morpholinyl, oxazolidinyl, isoxazolidinyl, piperidinyl, piperazinyl, methylpiperazinyl, N-methylpiperazinyl, pyrrolidinyl, pyrazolidinyl, tetrahydrofuranyl,
  • hydrazinyl as used herein, alone or in combination, refers to two amino groups joined by a single bond, i.e., —N—N—.
  • hydroxyalkyl refers to a hydroxy group attached to the parent molecular moiety through an alkyl group.
  • hydroxamic acid refers to —C( ⁇ O)NHOH, wherein the parent molecular moiety is attached to the hydroxamic acid group by means of the carbon atom.
  • main chain refers to the longest contiguous or adjacent chain of carbon atoms starting at the point of attachment of a group to the compounds of any one of the formulas disclosed herein.
  • linear chain of atoms refers to the longest straight chain of atoms independently selected from carbon, nitrogen, oxygen and sulfur.
  • lower means containing from 1 to and including 6 carbon atoms.
  • lower aryl as used herein, alone or in combination, means phenyl or naphthyl, which may be optionally substituted as provided.
  • lower heteroaryl means either 1) monocyclic heteroaryl comprising five or six ring members, of which between one and four said members may be heteroatoms chosen from O, S, and N, or 2) bicyclic heteroaryl, wherein each of the fused rings comprises five or six ring members, comprising between them one to four heteroatoms chosen from O, S, and N.
  • lower cycloalkyl means a monocyclic cycloalkyl having between three and six ring members. Lower cycloalkyls may be unsaturated. Examples of lower cycloalkyl include cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl.
  • lower heterocycloalkyl means a monocyclic heterocycloalkyl having between three and six ring members, of which between one and four may be heteroatoms chosen from O, S, and N.
  • Examples of lower heterocycloalkyls include pyrrolidinyl, imidazolidinyl, pyrazolidinyl, piperidinyl, piperazinyl, and morpholinyl.
  • Lower heterocycloalkyls may be unsaturated.
  • lower amino refers to —NRR, wherein R and R′ are independently chosen from hydrogen, lower alkyl, and lower heteroalkyl, any of which may be optionally substituted. Additionally, the R and R′ of a lower amino group may combine to form a five- or six-membered heterocycloalkyl, either of which may be optionally substituted.
  • nitro refers to —NO 2 .
  • oxy or “oxa,” as used herein, alone or in combination, refer to —O—.
  • perhaloalkoxy refers to an alkoxy group where all of the hydrogen atoms are replaced by halogen atoms.
  • perhaloalkyl refers to an alkyl group where all of the hydrogen atoms are replaced by halogen atoms.
  • phosphonate refers to a —P( ⁇ O)(OR) 2 group, wherein R is chosen from alkyl and aryl.
  • phosphonic acid refers to a —P( ⁇ O)(OH) 2 group.
  • sulfonate refers to the —SO 3 H group and its anion as the sulfonic acid is used in salt formation.
  • sulfonyl as used herein, alone or in combination, refers to —S(O) 2 —.
  • N-sulfonamido refers to a RS( ⁇ O) 2 NR′— group with R and R′ as defined herein.
  • S-sulfonamido refers to a —S( ⁇ O) 2 NRR′, group, with R and R′ as defined herein.
  • thia and thio refer to a —S— group or an ether wherein the oxygen is replaced with sulfur.
  • the oxidized derivatives of the thio group namely sulfinyl and sulfonyl, are included in the definition of thia and thio.
  • thiol as used herein, alone or in combination, refers to an —SH group.
  • thiocarbonyl when alone includes thioformyl —C(S)H and in combination is a —C(S)— group.
  • N-thiocarbamyl refers to an ROC(S)NR′— group, with R and R′ as defined herein.
  • O-thiocarbamyl refers to a —OC(S)NRR′, group with R and R′ as defined herein.
  • thiocyanato refers to a —CNS group.
  • trihalomethoxy refers to a X 3 CO— group where X is a halogen.
  • any definition herein may be used in combination with any other definition to describe a composite structural group.
  • the trailing element of any such definition is that which attaches to the parent moiety.
  • the composite group alkylamido would represent an alkyl group attached to the parent molecule through an amido group
  • the term alkoxyalkyl would represent an alkoxy group attached to the parent molecule through an alkyl group.
  • n When a group is defined to be “null,” what is meant is that said group is absent. Similarly, when a designation such as “n” which may be chosen from a group or range of integers is designated to be 0, then the group which it designates is either absent, if in a terminal position, or condenses to form a bond, if it falls between two other groups.
  • the term “optionally substituted” means the anteceding group may be substituted or unsubstituted.
  • the substituents of an “optionally substituted” group may include, without limitation, one or more substituents independently selected from the following groups or a particular designated set of groups, alone or in combination: lower alkyl, lower alkenyl, lower alkynyl, lower alkanoyl, lower heteroalkyl, lower heterocycloalkyl, lower haloalkyl, lower haloalkenyl, lower haloalkynyl, lower perhaloalkyl, lower perhaloalkoxy, lower cycloalkyl, phenyl, aryl, aryloxy, lower alkoxy, lower haloalkoxy, oxo, lower acyloxy, carbonyl, carboxyl, lower alkylcarbonyl, lower carboxyester, lower carboxamido, cyano, hydrogen, halogen, hydroxy, amino, lower alkylamino
  • Two substituents may be joined together to form a fused five-, six-, or seven-membered carbocyclic or heterocyclic ring consisting of zero to three heteroatoms, for example forming methylenedioxy or ethylenedioxy.
  • An optionally substituted group may be unsubstituted (e.g., —CH 2 CH 3 ), fully substituted (e.g., —CF 2 CF 3 ), monosubstituted (e.g., —CH 2 CH 2 F) or substituted at a level anywhere in-between fully substituted and monosubstituted (e.g., —CH 2 CF 3 ).
  • alkylene groups enclosed by ( ) m and ( ) n may be m or n carbons long.
  • R or the term R′ refers to a moiety chosen from hydrogen, alkyl, cycloalkyl, heteroalkyl, aryl, heteroaryl and heterocycloalkyl, any of which may be optionally substituted.
  • aryl, heterocycle, R, etc. occur more than one time in a formula or generic structure, its definition at each occurrence is independent of the definition at every other occurrence.
  • certain groups may be attached to a parent molecule or may occupy a position in a chain of elements from either end as written.
  • an unsymmetrical group such as —C(O)N(R)— may be attached to the parent moiety at either the carbon or the nitrogen.
  • bonds refers to a covalent linkage between two atoms, or two moieties when the atoms joined by the bond are considered to be part of larger substructure.
  • a bond may be single, double, or triple unless otherwise specified.
  • a dashed line between two atoms in a drawing of a molecule indicates that an additional bond may be present or absent at that position.
  • disease as used herein is intended to be generally synonymous, and is used interchangeably with, the terms “disorder” and “condition” (as in medical condition), in that all reflect an abnormal condition of the human or animal body or of one of its parts that impairs normal functioning, is typically manifested by distinguishing signs and symptoms, and causes the human or animal to have a reduced duration or quality of life.
  • combination therapy means the administration of two or more therapeutic agents to treat a therapeutic condition or disorder described in the present disclosure. Such administration encompasses co-administration of these therapeutic agents in a substantially simultaneous manner, such as in a single capsule having a fixed ratio of active ingredients or in multiple, separate capsules for each active ingredient. In addition, such administration also encompasses use of each type of therapeutic agent in a sequential manner. In either case, the treatment regimen will provide beneficial effects of the drug combination in treating the conditions or disorders described herein.
  • terapéuticaally effective is intended to qualify the amount of active ingredients used in the treatment of a disease or disorder. This amount will achieve the goal of reducing or eliminating the said disease or disorder.
  • terapéuticaally acceptable refers to those compounds (or salts, prodrugs, tautomers, zwitterionic forms, etc.) which are suitable for use in contact with the tissues of patients without undue toxicity, irritation, and allergic response, are commensurate with a reasonable benefit/risk ratio, and are effective for their intended use.
  • patient means all mammals including humans. Examples of patients include humans, cows, dogs, cats, goats, sheep, pigs, and rabbits. Preferably, the patient is a human.
  • prodrug refers to a compound that is made more active in vivo.
  • Certain compounds disclosed herein may also exist as prodrugs, as described in Hydrolysis in Drug and Prodrug Metabolism: Chemistry, Biochemistry, and Enzymology (Testa, Bernard and Mayer, Joachim M. Wiley-VHCA, Zurich, Switzerland 2003).
  • Prodrugs of the compounds described herein are structurally modified forms of the compound that readily undergo chemical changes under physiological conditions to provide the compound.
  • prodrugs can be converted to the compound by chemical or biochemical methods in an ex vivo environment. For example, prodrugs can be slowly converted to a compound when placed in a transdermal patch reservoir with a suitable enzyme or chemical reagent.
  • Prodrugs are often useful because, in some situations, they may be easier to administer than the compound, or parent drug. They may, for instance, be bioavailable by oral administration whereas the parent drug is not. The prodrug may also have improved solubility in pharmaceutical compositions over the parent drug.
  • a wide variety of prodrug derivatives are known in the art, such as those that rely on hydrolytic cleavage or oxidative activation of the prodrug.
  • An example, without limitation, of a prodrug would be a compound which is administered as an ester (the “prodrug”), but then is metabolically hydrolyzed to the carboxylic acid, the active entity. Additional examples include peptidyl derivatives of a compound.
  • the compounds disclosed herein can exist as therapeutically acceptable salts.
  • the present invention includes compounds listed above in the form of salts, including acid addition salts. Suitable salts include those formed with both organic and inorganic acids. Such acid addition salts will normally be pharmaceutically acceptable. However, salts of non-pharmaceutically acceptable salts may be of utility in the preparation and purification of the compound in question. Basic addition salts may also be formed and be pharmaceutically acceptable.
  • Pharmaceutical Salts Properties, Selection, and Use (Stahl, P. Heinrich. Wiley-VCHA, Zurich, Switzerland, 2002).
  • terapéuticaally acceptable salt represents salts or zwitterionic forms of the compounds disclosed herein which are water or oil-soluble or dispersible and therapeutically acceptable as defined herein.
  • the salts can be prepared during the final isolation and purification of the compounds or separately by reacting the appropriate compound in the form of the free base with a suitable acid.
  • Representative acid addition salts include acetate, adipate, alginate, L-ascorbate, aspartate, benzoate, benzenesulfonate (besylate), bisulfate, butyrate, camphorate, camphorsulfonate, citrate, digluconate, formate, fumarate, gentisate, glutarate, glycerophosphate, glycolate, hemisulfate, heptanoate, hexanoate, hippurate, hydrochloride, hydrobromide, hydroiodide, 2-hydroxyethansulfonate (isethionate), lactate, maleate, malonate, DL-mandelate, mesitylenesulfonate, methanesulfonate, naphthylenesulfonate, nicotinate, 2-naphthalenesulfonate, oxalate, pamoate, pectinate, persulfate, 3-phenyl
  • basic groups in the compounds disclosed herein can be quaternized with methyl, ethyl, propyl, and butyl chlorides, bromides, and iodides; dimethyl, diethyl, dibutyl, and diamyl sulfates; decyl, lauryl, myristyl, and steryl chlorides, bromides, and iodides; and benzyl and phenethyl bromides.
  • acids which can be employed to form therapeutically acceptable addition salts include inorganic acids such as hydrochloric, hydrobromic, sulfuric, and phosphoric, and organic acids such as oxalic, maleic, succinic, and citric. Salts can also be formed by coordination of the compounds with an alkali metal or alkaline earth ion.
  • the present invention contemplates sodium, potassium, magnesium, and calcium salts of the compounds disclosed herein, and the like.
  • Basic addition salts can be prepared during the final isolation and purification of the compounds by reaction of a carboxy group with a suitable base such as the hydroxide, carbonate, or bicarbonate of a metal cation or with ammonia or an organic primary, secondary, or tertiary amine.
  • a suitable base such as the hydroxide, carbonate, or bicarbonate of a metal cation or with ammonia or an organic primary, secondary, or tertiary amine.
  • the cations of therapeutically acceptable salts include lithium, sodium, potassium, calcium, magnesium, and aluminum, as well as nontoxic quaternary amine cations such as ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, diethylamine, ethylamine, tributylamine, pyridine, N,N-dimethylaniline, N-methylpiperidine, N-methylmorpholine, dicyclohexylamine, procaine, dibenzylamine, N,N-dibenzylphenethylamine, 1-ephenamine, and N,N′-dibenzylethylenediamine.
  • Other representative organic amines useful for the formation of base addition salts include ethylenediamine, ethanolamine, diethanolamine, piperidine, and piperazine.
  • a salt of a compound can be made by reaction of the appropriate compound, in the form of the free base, with the appropriate acid.
  • the compounds disclosed herein can exist as polymorphs and other distinct solid forms such as solvates, hydrates, and the like.
  • a compound may be a polymorph, solvate, or hydrate of a salt or of the free base or acid.
  • compositions which comprise one or more of certain compounds disclosed herein, or one or more pharmaceutically acceptable salts, esters, prodrugs, amides, or solvates thereof, together with one or more pharmaceutically acceptable carriers thereof and optionally one or more other therapeutic ingredients.
  • the carrier(s) must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not deleterious to the recipient thereof. Proper formulation is dependent upon the route of administration chosen.
  • compositions disclosed herein may be manufactured in any manner known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or compression processes.
  • the formulations include those suitable for oral, parenteral (including subcutaneous, intradermal, intramuscular, intravenous, intraarticular, intraadiposal, intraarterial, intracranial, intralesional, intranasal, intraocular, intrapericardial, intraperitoneal, intrapleural, intraprostatical, intrarectal, intrathecal, intratracheal, intratumoral, intraumbilical, intravaginal, intravesicular, intravitreal, and intramedullary), intraperitoneal, rectal, topical (including, without limitation, dermal, buccal, sublingual, vaginal, rectal, nasal, otic, and ocular), local, mucosal, sublingual, subcutaneous, transmucosal, transdermal, transbuccal, transdermal, and vaginal; liposomal, in cremes, in lipid compositions, via a catheter, via a lavage, via continuous infusion, via infusion, via inhalation, via injection, via local delivery, via
  • formulations may conveniently be presented in unit dosage form and may be prepared by any of the methods well known in the art of pharmacy. Typically, these methods include the step of bringing into association a compound disclosed herein or a pharmaceutically acceptable salt, ester, amide, prodrug or solvate thereof (“active ingredient”) with the carrier which constitutes one or more accessory ingredients.
  • active ingredient a compound disclosed herein or a pharmaceutically acceptable salt, ester, amide, prodrug or solvate thereof
  • the formulations are prepared by uniformly and intimately bringing into association the active ingredient with liquid carriers or finely divided solid carriers or both and then, if necessary, shaping the product into the desired formulation.
  • Formulations of the compounds disclosed herein suitable for oral administration may be presented as discrete units such as hard or soft capsules, wafers, cachets or tablets each containing a predetermined amount of the active ingredient; as a powder or granules; as a syrup, elixir, solution, or a suspension in an aqueous liquid or a non-aqueous liquid; or as an oil-in-water liquid emulsion, a water-in-oil liquid emulsion, or a compound dispersed in a liposome.
  • the active ingredient may also be presented as a bolus, electuary or paste.
  • compositions that can be used orally include tablets, push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. Tablets may be made by compression or molding, optionally with one or more accessory ingredients. Compressed tablets may be prepared by compressing in a suitable machine the active ingredient in a free-flowing form such as a powder or granules, optionally mixed with binders, inert diluents, or lubricating, surface active or dispersing agents. Molded tablets may be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent.
  • the tablets may optionally be coated or scored and may be formulated to provide delayed, slowed, or controlled release or absorption of the active ingredient therein.
  • Compositions may further comprise an agent that enhances solubility or dispersability. All formulations for oral administration should be in dosages suitable for such administration.
  • the push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers.
  • the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols.
  • stabilizers may be added. Dragee cores are provided with suitable coatings.
  • concentrated sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
  • Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.
  • the compounds, or granules or particles thereof may be coated in a material to protect the compounds from the action of acids and other natural conditions that may inactivate the compounds.
  • the compounds may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion, either to the body or to the site of a disease or wound.
  • Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative.
  • the compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
  • the formulations may be presented in unit-dose or multi-dose containers, for example sealed ampoules and vials, and may be stored in powder form or in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example, saline or sterile pyrogen-free water, immediately prior to use.
  • sterile liquid carrier for example, saline or sterile pyrogen-free water
  • Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets of the kind previously described.
  • Formulations for parenteral administration include aqueous and non-aqueous (oily) sterile injection solutions of the active compounds which may contain antioxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents and thickening agents.
  • Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes.
  • Aqueous injection suspensions may contain substances that increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran.
  • the suspension may also contain suitable stabilizers or agents that increase the solubility of the compounds to allow for the preparation of highly concentrated solutions.
  • suitable stabilizers or agents that increase the solubility of the compounds to allow for the preparation of highly concentrated solutions.
  • the compounds may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection.
  • the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.
  • compositions may take the form of tablets, lozenges, pastilles, or gels formulated in conventional manner.
  • Such compositions may comprise the active ingredient in a flavored basis such as sucrose and acacia or tragacanth.
  • the compounds may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter, polyethylene glycol, or other glycerides.
  • Certain compounds disclosed herein may be administered topically, that is by non-systemic administration. This includes the application of a compound disclosed herein externally to the epidermis or the buccal cavity and the instillation of such a compound into the ear, eye and nose, such that the compound does not significantly enter the blood stream.
  • systemic administration refers to oral, intravenous, intraperitoneal and intramuscular administration.
  • Formulations suitable for topical administration include liquid or semi-liquid preparations suitable for penetration through the skin to the site of inflammation such as gels, liniments, lotions, creams, ointments or pastes, and drops suitable for administration to the eye, ear or nose.
  • the active ingredient for topical administration may comprise, for example, from 0.001% to 10% w/w (by weight) of the formulation. In certain embodiments, the active ingredient may comprise as much as 10% w/w. In other embodiments, it may comprise less than 5% w/w. In certain embodiments, the active ingredient may comprise from 2% w/w to 5% w/w. In other embodiments, it may comprise from 0.1% to 1% w/w of the formulation.
  • Topical ophthalmic, otic, and nasal formulations disclosed herein may comprise excipients in addition to the active ingredient.
  • Excipients commonly used in such formulations include, but are not limited to, tonicity agents, preservatives, chelating agents, buffering agents, and surfactants.
  • Other excipients comprise solubilizing agents, stabilizing agents, comfort-enhancing agents, polymers, emollients, pH-adjusting agents and/or lubricants.
  • excipients may be used in formulations disclosed herein including water, mixtures of water and water-miscible solvents, such as C1-C7-alkanols, vegetable oils or mineral oils comprising from 0.5 to 5% non-toxic water-soluble polymers, natural products, such as alginates, pectins, tragacanth, karaya gum, guar gum, xanthan gum, carrageenan, agar and acacia, starch derivatives, such as starch acetate and hydroxypropyl starch, and also other synthetic products such as polyvinyl alcohol, polyvinylpyrrolidone, polyvinyl methyl ether, polyethylene oxide, preferably cross-linked polyacrylic acid and mixtures of those products.
  • concentration of the excipient is, typically, from 1 to 100,000 times the concentration of the active ingredient.
  • the excipients to be included in the formulations are typically selected because of their inertness towards the active ingredient component of the formulation
  • suitable tonicity-adjusting agents include, but are not limited to, mannitol, sodium chloride, glycerin, sorbitol and the like.
  • Suitable buffering agents include, but are not limited to, phosphates, borates, acetates and the like.
  • Suitable surfactants include, but are not limited to, ionic and nonionic surfactants (though nonionic surfactants are preferred), RLM 100, POE 20 cetylstearyl ethers such as Procol® CS20 and poloxamers such as Pluronic® F68.
  • the formulations set forth herein may comprise one or more preservatives.
  • preservatives include p-hydroxybenzoic acid ester, sodium perborate, sodium chlorite, alcohols such as chlorobutanol, benzyl alcohol or phenyl ethanol, guanidine derivatives such as polyhexamethylene biguanide, sodium perborate, polyquarternium-1, amino alcohols such as AMP-95, or sorbic acid.
  • the formulation may be self-preserved so that no preservation agent is required.
  • formulations are prepared using a buffering system that maintains the formulation at a pH of about 4.5 to a pH of about 8. In further embodiments, the pH is from 7 to 8.
  • Gels for topical or transdermal administration may comprise, generally, a mixture of volatile solvents, nonvolatile solvents, and water.
  • the volatile solvent component of the buffered solvent system may include lower (C1-C6) alkyl alcohols, lower alkyl glycols and lower glycol polymers.
  • the volatile solvent is ethanol.
  • the volatile solvent component is thought to act as a penetration enhancer, while also producing a cooling effect on the skin as it evaporates.
  • the nonvolatile solvent portion of the buffered solvent system is selected from lower alkylene glycols and lower glycol polymers. In certain embodiments, propylene glycol is used.
  • the nonvolatile solvent slows the evaporation of the volatile solvent and reduces the vapor pressure of the buffered solvent system.
  • the amount of this nonvolatile solvent component, as with the volatile solvent, is determined by the pharmaceutical compound or drug being used. When too little of the nonvolatile solvent is in the system, the pharmaceutical compound may crystallize due to evaporation of volatile solvent, while an excess may result in a lack of bioavailability due to poor release of drug from solvent mixture.
  • the buffer component of the buffered solvent system may be selected from any buffer commonly used in the art; in certain embodiments, water is used. A common ratio of ingredients is about 20% of the nonvolatile solvent, about 40% of the volatile solvent, and about 40% water. Several optional ingredients can be added to the topical composition.
  • gelling agents can include, but are not limited to, semisynthetic cellulose derivatives (such as hydroxypropylmethylcellulose) and synthetic polymers, galactomannan polymers (such as guar and derivatives thereof), and cosmetic agents.
  • Lotions include those suitable for application to the skin or eye.
  • An eye lotion may comprise a sterile aqueous solution optionally containing a bactericide and may be prepared by methods similar to those for the preparation of drops.
  • Lotions or liniments for application to the skin may also include an agent to hasten drying and to cool the skin, such as an alcohol or acetone, and/or a moisturizer such as glycerol or an oil such as castor oil or arachis oil.
  • Creams, ointments or pastes are semi-solid formulations of the active ingredient for external application. They may be made by mixing the active ingredient in finely-divided or powdered form, alone or in solution or suspension in an aqueous or non-aqueous fluid, with the aid of suitable machinery, with a greasy or non-greasy base.
  • the base may comprise hydrocarbons such as hard, soft or liquid paraffin, glycerol, beeswax, a metallic soap; a mucilage; an oil of natural origin such as almond, corn, arachis, castor or olive oil; wool fat or its derivatives or a fatty acid such as stearic or oleic acid together with an alcohol such as propylene glycol or a macrogel.
  • the formulation may incorporate any suitable surface active agent such as an anionic, cationic or non-ionic surfactant such as a sorbitan ester or a polyoxyethylene derivative thereof.
  • suitable surface active agent such as an anionic, cationic or non-ionic surfactant such as a sorbitan ester or a polyoxyethylene derivative thereof.
  • Suspending agents such as natural gums, cellulose derivatives or inorganic materials such as silicaceous silicas, and other ingredients such as lanolin, may also be included.
  • Drops may comprise sterile aqueous or oily solutions or suspensions and may be prepared by dissolving the active ingredient in a suitable aqueous solution of a bactericidal and/or fungicidal agent and/or any other suitable preservative, and, in certain embodiments, including a surface active agent.
  • the resulting solution may then be clarified by filtration, transferred to a suitable container which is then sealed and sterilized by autoclaving or maintaining at 98-100° C. for half an hour.
  • the solution may be sterilized by filtration and transferred to the container by an aseptic technique.
  • bactericidal and fungicidal agents suitable for inclusion in the drops are phenylmercuric nitrate or acetate (0.002%), benzalkonium chloride (0.01%) and chlorhexidine acetate (0.01%).
  • Suitable solvents for the preparation of an oily solution include glycerol, diluted alcohol and propylene glycol.
  • Formulations for topical administration in the mouth include lozenges comprising the active ingredient in a flavored basis such as sucrose and acacia or tragacanth, and pastilles comprising the active ingredient in a basis such as gelatin and glycerin or sucrose and acacia.
  • compounds may be conveniently delivered from an insufflator, nebulizer pressurized packs or other convenient means of delivering an aerosol spray.
  • Pressurized packs may comprise a suitable propellant such as dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas.
  • the dosage unit may be determined by providing a valve to deliver a metered amount.
  • the compounds according to the invention may take the form of a dry powder composition, for example, a powder mix of the compound and a suitable powder base such as lactose or starch.
  • the powder composition may be presented in unit dosage form, in for example, capsules, cartridges, gelatin or blister packs from which the powder may be administered with the aid of an inhalator or insufflator.
  • the therapeutic compound may also be administered intraspinally or intracerebrally.
  • Dispersions for these types of administrations can be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations may contain a preservative to prevent the growth of microorganisms.
  • compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion.
  • the composition must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (such as, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils.
  • the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • a coating such as lecithin
  • surfactants for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars, sodium chloride, or polyalcohols such as mannitol and sorbitol, in the composition.
  • Sterile injectable solutions can be prepared by incorporating the therapeutic compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the therapeutic compound into a sterile carrier that contains a basic dispersion medium and required other ingredients to be pharmacologically sound.
  • the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient (i.e., the therapeutic compound) plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • Dosage unit form refers to physically discrete units suited as unitary dosages for the subjects to be treated; each unit containing a predetermined quantity of therapeutic compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
  • the specification for the dosage unit forms of the invention are dictated by and directly dependent on (a) the unique characteristics of the therapeutic compound and the particular therapeutic effect to be achieved, and (b) the limitations inherent in the art of compounding such a therapeutic compound for the treatment of a selected condition in a patient.
  • formulations described above may include other agents conventional in the art having regard to the type of formulation in question, for example, those suitable for oral administration may include flavoring agents.
  • Compounds may be administered at a dose of from 0.1 to 500 mg/kg per day.
  • the dose range for adult humans is generally from 5 mg to 2 g/day.
  • Tablets or other forms of presentation provided in discrete units may conveniently contain an amount of one or more compounds which is effective at such dosage or as a multiple of the same, for instance, units containing 5 mg to 500 mg, usually around 10 mg to 200 mg.
  • Preferred unit dosage formulations are those containing an effective dose, as herein below recited, or an appropriate fraction thereof, of the active ingredient.
  • a formulation disclosed herein is administered once a day.
  • the formulations may also be formulated for administration at any frequency of administration, including once a week, once every 5 days, once every 3 days, once every 2 days, twice a day, three times a day, four times a day, five times a day, six times a day, eight times a day, every hour, or any greater frequency.
  • Such dosing frequency is also maintained for a varying duration of time depending on the therapeutic regimen.
  • the duration of a particular therapeutic regimen may vary from one-time dosing to a regimen that extends for months or years.
  • the formulations are administered at varying dosages, but typical dosages are one to two drops at each administration, or a comparable amount of a gel or other formulation.
  • One of ordinary skill in the art would be familiar with determining a therapeutic regimen for a specific indication.
  • the amount of active ingredient that may be combined with the carrier materials to produce a single dosage form will vary depending upon the host treated and the particular mode of administration. Similarly, the precise amount of compound administered to a patient will be the responsibility of the attendant physician.
  • the specific dose level for any particular patient will depend upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, sex, diets, time of administration, route of administration, rate of excretion, drug combination, the precise disorder being treated, and the severity of the indication or condition being treated.
  • the route of administration may vary depending on the condition and its severity.
  • the compounds described herein may be administered in combination with another therapeutic agent.
  • another therapeutic agent such as a pharmaceutically acceptable salt, ester, or prodrug thereof.
  • an adjuvant i.e., by itself the adjuvant may only have minimal therapeutic benefit, but in combination with another therapeutic agent, the overall therapeutic benefit to the patient is enhanced.
  • the benefit experienced by a patient may be increased by administering one of the compounds described herein with another therapeutic agent (which also includes a therapeutic regimen) that also has therapeutic benefit.
  • another therapeutic agent which also includes a therapeutic regimen
  • increased therapeutic benefit may result by also providing the patient with another therapeutic agent for sickle cell anemia or for acute myelogenous leukemia.
  • the overall benefit experienced by the patient may simply be additive of the two therapeutic agents or the two agents may have synergistic therapeutic effects in a patient.
  • Effective combination therapy may be achieved with a single composition or pharmacological formulation that includes both agents, or with two distinct compositions or formulations, at the same time, wherein one composition includes a compound of the present disclosure, and the other includes the second agent(s).
  • the therapy may precede or follow the other agent treatment by intervals ranging from minutes to months.
  • Administration of the compounds of the present disclosure to a patient will follow general protocols for the administration of pharmaceuticals, taking into account the toxicity, if any, of the drug. It is expected that the treatment cycles would be repeated as necessary.
  • agents that inhibit DNA methyltransferases such as decitabine or 5′-aza-cytadine
  • agents that inhibit the activity of histone deacetylases, histone de-sumoylases, histone de-ubiquitinases, or histone phosphatases such as hydroxyurea
  • antisense RNAs that might inhibit the expression of other components of the protein complex bound at the DR site in the gamma globin promoter
  • agents that inhibit the action of Klf1 or the expression of KLF1 agents that inhibit the action of Bcl11a or the expression of BCL11A
  • agents that inhibit cell cycle progression such as hydroxyurea, ara-C or daunorubicin
  • agents that induce differentiation in leukemic cells such as all-trans retinoic acid (ATRA).
  • ATRA all-trans retinoic acid
  • the present invention provides methods for treating diseases or disorders in a human or animal subject in need of such treatment comprising administering to said subject an amount of a compound disclosed herein effective to reduce or prevent said disorder in the subject, optionally in combination with at least one additional agent for the treatment of said disorder that is known in the art.
  • the compounds disclosed herein are useful in the prevention and/or treatment of beta-hemoglobinopathies such as thalassemia major, sickle cell disease, hemoglobin E/thalassemia, and thalassemia intermedia.
  • the compounds disclosed herein can be used in the treatment of diseases in which an increase in transcription through the manipulation of epigenetic regulatory factors such as inhibition of KDM1A would be beneficial to the patient.
  • diseases including but not limited to loss of function mutations, mutations resulting in haploinsufficiency, deletions and duplications of genetic material or epigenetic regulatory mechanisms have altered the normal expression pattern of a gene or genes that has the effect of altering the dose of a gene product(s).
  • Such diseases may include diseases both acquired and hereditary in which the expression of, for example, cytokines affecting immune function, are altered, X-linked mental retardation and other forms of compromised cognitive or motor function such as Alzheimer and Parkinson disease whether they are the acquired or hereditary forms, lipid disorders such as elevated cholesterol, low density lipoprotein, very low density lipoprotein or triglycerides, both type one and type two diabetes, and Mendelian genetic diseases.
  • diseases both acquired and hereditary in which the expression of, for example, cytokines affecting immune function, are altered, X-linked mental retardation and other forms of compromised cognitive or motor function such as Alzheimer and Parkinson disease whether they are the acquired or hereditary forms, lipid disorders such as elevated cholesterol, low density lipoprotein, very low density lipoprotein or triglycerides, both type one and type two diabetes, and Mendelian genetic diseases.
  • Inflammatory conditions include, without limitation: arthritis, including sub-types and related conditions such as rheumatoid arthritis, spondyloarthropathies, gouty arthritis, osteoarthritis, systemic lupus erythematosus, juvenile arthritis, acute rheumatic arthritis, enteropathic arthritis, neuropathic arthritis, psoriatic arthritis, and pyogenic arthritis; osteoporosis, tendonitis, bursitis, and other related bone and joint disorders; gastrointestinal conditions such as reflux esophagitis, diarrhea, inflammatory bowel disease, Crohn's disease, gastritis, irritable bowel syndrome, ulcerative colitis, acute and chronic inflammation of the pancreas; pulmonary inflammation, such as that associated with viral infections and cystic fibrosis; skin-related conditions such as psoriasis, eczema, burns, sunburn, dermatitis (
  • Autoimmune disorders may be ameliorated by the treatment with compounds disclosed herein.
  • Autoimmune disorders include Crohn's disease, ulcerative colitis, dermatitis, dermatomyositis, diabetes mellitus type 1, Goodpasture's syndrome, Graves' disease, Guillain-Barré syndrome (GBS), autoimmune encephalomyelitis, Hashimoto's disease, idiopathic thrombocytopenic purpura, lupus erythematosus, mixed connective tissue disease, multiple sclerosis (MS), myasthenia gravis, narcolepsy, pemphigus vulgaris, pernicious anemia, psoriasis, psoriatic arthritis, polymyositis, primary biliary cirrhosis, rheumatoid arthritis, Sjögren's syndrome, scleroderma, temporal arteritis (also known as “giant cell arteritis”), vasculitis, and Wege
  • the compounds disclosed herein are also useful for the treatment of organ and tissue injury associated with severe burns, sepsis, trauma, wounds, and hemorrhage- or resuscitation-induced hypotension, and also in such diseases as vascular diseases, migraine headaches, periarteritis nodosa, thyroiditis, aplastic anemia, Hodgkin's disease, scleredoma, rheumatic fever, type I diabetes, neuromuscular junction disease including myasthenia gravis, white matter disease including multiple sclerosis, sarcoidosis, nephritis, nephrotic syndrome, Behcet's syndrome, polymyositis, gingivitis, periodontis, swelling occurring after injury, ischemias including myocardial ischemia, cardiovascular ischemia, and ischemia secondary to cardiac arrest, and the like.
  • diseases as vascular diseases, migraine headaches, periarteritis nodosa, thyroiditis, aplastic anemia, Hodgkin
  • the compounds disclosed herein are also useful for the treatment of certain diseases and disorders of the nervous system.
  • Central nervous system disorders in KDM1A inhibition is useful include cortical dementias including Alzheimer's disease, central nervous system damage resulting from stroke, ischemias including cerebral ischemia (both focal ischemia, thrombotic stroke and global ischemia (for example, secondary to cardiac arrest), and trauma.
  • Neurodegenerative disorders in which KDM1A inhibition is useful include nerve degeneration or nerve necrosis in disorders such as hypoxia, hypoglycemia, epilepsy, and in cases of central nervous system (CNS) trauma (such as spinal cord and head injury), hyperbaric oxygen-induced convulsions and toxicity, dementia e.g., pre-senile dementia, and AIDS-related dementia, cachexia, Sydenham's chorea, Huntington's disease, Parkinson's Disease, amyotrophic lateral sclerosis (ALS), Korsakoff's disease, cognitive disorders relating to a cerebral vessel disorder, hypersensitivity, sleeping disorders, schizophrenia, depression, depression or other symptoms associated with Premenstrual Syndrome (PMS), and anxiety.
  • CNS central nervous system
  • PMS Premenstrual Syndrome
  • Still other disorders or conditions advantageously treated by the compounds disclosed herein include the prevention or treatment of hyperproliferative diseases, especially cancers, either alone or in combination with standards of care especially those agents that target tumor growth by re-instating tumor suppressor genes in the malignant cells.
  • Hematological and non-hematological malignancies which may be treated or prevented include but are not limited to multiple myeloma, acute and chronic leukemias and hematopoietic proliferative and neoplastic disorders including Myelodysplastic Syndrome (MDS), Acute Myelogenous Leukemia (AML), Acute Lymphocytic Leukemia (ALL), Chronic Lymphocytic Leukemia (CLL), and Chronic Myelogenous Leukemia (CML), lymphomas, including Hodgkin's lymphoma and non-Hodgkin's lymphoma (low, intermediate, and high grade), as well as solid tumors and malignancies of the brain, head and neck, breast, lung (including non-small-cell
  • the present compounds and methods can also be used to treat fibrosis, such as that which occurs with radiation therapy.
  • the present compounds and methods can be used to treat subjects having or prevent the progression of adenomatous polyps, including those with familial adenomatous polyposis (FAP) or sarcoidosis.
  • Non-cancerous proliferative disorders additionally include psoriasis, eczema, and dermatitis.
  • the present compounds may also be used in co-therapies, partially or completely, in place of other conventional anti-inflammatory therapies, such as together with steroids, NSAIDs, COX-2 selective inhibitors, 5-lipoxygenase inhibitors, LTB 4 antagonists and LTA 4 hydrolase inhibitors.
  • the compounds disclosed herein may also be used to prevent tissue damage when therapeutically combined with antibacterial or antiviral agents.
  • KDM1A using flavin adenosine dinucleotide (FAD) as a cofactor, epigenetically regulates energy-expenditure genes in adipocytes depending on the cellular FAD availability. Additionally, loss of KDM1A function induces a number of regulators of energy expenditure and mitochondrial metabolism resulting in the activation of mitochondrial respiration. Furthermore, in the adipose tissues from mice fed a high-fat diet, expression of KDM1A-target genes is reduced.
  • FAD flavin adenosine dinucleotide
  • Metabolic syndrome (also known as metabolic syndrome X) is characterized by having at least three of the following symptoms: insulin resistance; abdominal fat—in men this is defined as a 40 inch waist or larger, in women 35 inches or larger; high blood sugar levels—at least 110 milligrams per deciliter (mg/dL) after fasting; high triglycerides—at least 150 mg/dL in the blood stream; low HDL—less than 40 mg/dL; pro-thrombotic state (e.g., high fibrinogen or plasminogen activator inhibitor in the blood); or blood pressure of 130/85 mmHg or higher.
  • a connection has been found between metabolic syndrome and other conditions such as obesity, high blood pressure and high levels of LDL cholesterol, all of which are risk factors for cardiovascular diseases. For example, an increased link between metabolic syndrome and atherosclerosis has been shown. People with metabolic syndrome are also more prone to developing type 2 diabetes, as well as PCOS (polycystic ovarian syndrome) in women and prostate cancer in men.
  • Type 2 diabetes is the condition most obviously linked to insulin resistance.
  • Compensatory hyperinsulinemia helps maintain normal glucose levels often for decades before overt diabetes develops.
  • beta cells of the pancreas are unable to overcome insulin resistance through hypersecretion.
  • Glucose levels rise and a diagnosis of diabetes can be made.
  • Patients with type 2 diabetes remain hyperinsulinemic until they are in an advanced stage of disease.
  • insulin resistance can also correlate with hypertension.
  • One half of patients with essential hypertension are insulin resistant and hyperinsulinemic, and there is evidence that blood pressure is linked to the degree of insulin resistance. Hyperlipidemia, too, is associated with insulin resistance.
  • the lipid profile of patients with type 2 diabetes includes increased serum very-low-density lipoprotein (VLDL) cholesterol and triglyceride levels and, sometimes, a decreased low-density lipoprotein (LDL) cholesterol level.
  • VLDL very-low-density lipoprotein
  • LDL low-density lipoprotein
  • Insulin resistance has been found in persons with low levels of high-density lipoprotein HDL). Insulin levels have also been linked to VLDL synthesis and plasma triglyceride levels.
  • Specific metabolic diseases and symptoms to be treated by the compounds, compositions, and methods disclosed herein are those mediated at least in part by KDM1A. Accordingly, disclosed herein are methods: for treating insulin resistance in a subject; for reducing glycogen accumulation in a subject; for raising HDL or HDLc, lowering LDL or LDLc, shifting LDL particle size from small dense to normal LDL, lowering VLDL, lowering triglycerides, or inhibiting cholesterol absorption in a subject; for reducing insulin resistance, enhancing glucose utilization or lowering blood pressure in a subject; for reducing visceral fat in a subject; for reducing serum transaminases in a subject; for inducing mitochondrial respiration in a subject; or for treating disease; all comprising the administration of a therapeutic amount of a compound as described herein, to a patient in need thereof.
  • the disease to be treated may be a metabolic disease.
  • the metabolic disease may be selected from the group consisting of: obesity, diabetes mellitus, especially Type 2 diabetes, hyperinsulinemia, glucose intolerance, metabolic syndrome X, dyslipidemia, hypertriglyceridemia, hypercholesterolemia, and hepatic steatosis.
  • the disease to be treated may be selected from the group consisting of: cardiovascular diseases including vascular disease, atherosclerosis, coronary heart disease, cerebrovascular disease, heart failure and peripheral vessel disease.
  • the methods above do not result in the induction or maintenance of a hypoglycemic state.
  • certain compounds and formulations disclosed herein may also be useful for veterinary treatment of companion animals, exotic animals and farm animals, including mammals, rodents, and the like. More preferred animals include horses, dogs, and cats.
  • PTFE polytetrafluoroethylene
  • RM Reaction Mixture
  • R H Relative Humidity
  • RT Room Temperature
  • SM Startting Material
  • MeCN acetonitrile
  • ClPh chlorophenol
  • DCE dichloroethane
  • DCM diichloromethane
  • DIPE di-isopropylether
  • DMA dimethyl acetamide
  • DMF dimethyl formamide
  • DMSO dimethylsulfoxide
  • Et 2 O diethyl ether
  • EtOAc ethyl acetate
  • EtOH ethanol
  • H 2 O water
  • I PA propan-2-ol
  • i-PrOAc iso-propyl acetate
  • MEK methyl ethyl ketone
  • MeOH methanol
  • MIBK methyl isobutyl ketone
  • MTBE methyl tert-butybutyl
  • the crude product (5 mL) was purified by Prep-HPLC with the following conditions (2#-AnalyseHPLC-SHIMADZU (HPLC-10)): Column, XBridge C18 OBD Prep Column, 100? 10 ⁇ m, 19 mm ⁇ 250 mm; mobile phase, Waters (10 MMOL/L NH4HCO3) and ACN—Waters (20.0% ACN—Waters up to 60.0% in 6 min); Detector, uv 254/220 nm. 150 mL product was obtained. This resulted in 330 mg (66%) of 1 as a white solid.
  • the method used to prepare 206 was used with the compound from the previous step (5 g, 9.29 mmol, 1.00 equiv) and thiomorpholine-1,1-dioxide hydrochloride (2.4 g, 13.98 mmol, 1.50 equiv) to afford 5 g (83.3%) of the product as a off-white solid.
  • the method used to prepare 201 was used with the compound from the previous step (5 g, 18.10 mmol), affording 5 g (94%) of the product as a light yellow solid.
  • the method used to prepare 209 was used with the product from the previous step (1.5 g, 7.38 mmol, 1.00 equiv) to afford 1.2 g (86%) of the product as a yellow solid.
  • the method used to prepare 203 was used with (2S)-5-[[(1R,2S)-2-(4-fluorophenyl)cyclopropyl](prop-2-en-1-yl)amino]-2-aminopentanoic acid (800 mg, 2.61 mmol, 1.00 equiv) and 4-(1H-1,2,3-triazol-1-yl)benzoyl chloride (800 mg, 3.85 mmol, 1.50 equiv) to afford 550 mg (44%) of the product as a yellow solid.
  • the method used to prepare 206 was used with the compound from the previous step (250 mg, 0.52 mmol, 1.00 equiv) and 4-(tert-butyloxycarbonyl)piperazine (148 mg, 0.79 mmol, 1.50 equiv) to afford 210 mg (62%) of the product as a yellow solid.
  • the method used to prepare 210 was used with the compound produced in the previous step (301 mg, 0.56 mmol, 1.00 equiv) to afford 72.1 mg (26%) of 35 as an off-white solid.
  • the method used to prepare 210 was used with the compound produced in the previous step (280 mg, 0.43 mmol) to afford 0.2 g (76%) of the product as a yellow solid.
  • the method used to prepare 210 was used with the compound produced in the previous step (180 mg, 0.30 mmol) to afford 100 mg (60%) of the product as an orange oil.
  • the method used to prepare 210 was used with the compound produced in the previous step (480 mg, 0.93 mmol) to afford 46.7 mg (11%) of 92 as a light yellow solid.
  • the method used to prepare 211 was used with 4-(methoxycarbonyl)benzoic acid (231.4 mg, 1.28 mmol, 1.00 equiv) and (2S)-2-amino-5-[[(1R,2S)-2-(4-fluorophenyl)cyclopropyl](prop-2-en-1-yl)amino]-1-(4-hydroxypiperidin-1-yl)pentan-1-one (500 mg, 1.28 mmol, 1.00 equiv) to afford 420 mg (59%) of the product as a light yellow oil.
  • the method used to prepare 210 was used with the compound produced in the previous step (420 mg, 0.76 mmol) to afford 650 mg (99%) of the product as an orange oil.
  • the method used to prepare 211 was used with 2-[[(tert-butoxy)carbonyl]amino]-5-[[2-(4-fluorophenyl)cyclopropyl](prop-2-en-1-yl)amino]pentanoic acid (1 g, 2.46 mmol, 1.00 equiv) and 1-methylpiperazine (500 mg, 4.99 mmol, 2.00 equiv) to afford in 1.1 g (95%) of the product as off-white oil.
  • the method used to prepare 210 was used with the compound produced in the previous step (1.2 g, 2.14 mmol) to afford 15.1 mg (1%) of 110 as a white solid.
  • the method used to prepare 206 was used with (2S)-2-[[(tert-butoxy)carbonyl]amino]-5-[[(2S)-2-(4-fluorophenyl)-cyclopropyl](prop-2-en-1-yl)amino]pentanoic acid (900 mg, 2.21 mmol, 1.00 equiv) and piperidin-4-ol (335 mg, 3.31 mmol, 1.50 equiv) to afford 1.2 g (98%) of the product as light yellow oil.
  • the method used to prepare 1 was used with the compound produced in the previous step (1.2 g, 2.45 mmol, 1.00 equiv) to afford 880 mg (71%) of the product as a yellow oil.
  • the method used to prepare 211 was used with the compound produced in the previous step (400 g, 794.39 mmol, 1.00 equiv), and 4-(1H-1,2,3-triazol-1-yl)benzoic acid (205 mg, 1.08 mmol) to afford 300 mg of the product as a yellow solid.
  • the method used to prepare 210 was used with the compound produced in the previous step (300 mg, 0.54 mmol) to afford (23%) of 111 as an off-white solid.
  • the method used to prepare 211 was used with the compound produced in the previous step (470 mg, 1.21 mmol, 1.00 equiv). to afford 608 mg (90%) of the product as a light yellow solid.
  • the method used to prepare 210 was used with the compound produced in the previous step (978 mg, 1.75 mmol, 1.00 equiv) to afford 61.0 mg (7%) of 117 as an off-white solid.
  • the method used to prepare 206 was used with the compound produced in the previous step (2.5 g, 7.53 mmol, 1.00 equiv) in and 1-methylpiperazine (1.13 g, 11.30 mmol, 1.50 equiv) to afford 2 g (64%) of the product as a yellow oil.
  • the method to prepare 205 was used with the compound produced in the previous step (2 g, 4.83 mmol) to afford 1.8 g (93%) of the product as an off-white solid.
  • the method used to prepare 208 was used with the compound produced in the previous step (200 mg, 0.52 mmol, 1.00 equiv) to afford 150 mg (75%) of the product as an off-white solid.
  • the method used to prepare 211 was used with the compound produced in the previous step (160 mg, 0.77 mmol, 1.00 equiv) and (2S)-2-amino-5-[[(1R,2S)-2-(4-fluorophenyl)cyclopropyl](prop-2-en-1-yl)amino]-1-(4-methylpiperazin-1-yl)pentan-1-one (300 mg, 0.77 mmol, 1.00 equiv) to afford 250 mg (56%) of the product as a yellow solid.
  • the method used to prepare 210 was used with the compound produced in the previous step (250 mg, 0.43 mmol) to afford 33.2 mg (14%) of 130 as a light brown solid.
  • the method used to prepare 210 was used with the compound from the previous step to afford 40.7 mg (5%) of the product as a white solid.
  • the method used to prepare 204 was used with the compound from the previous step (19.1 g, 54.99 mmol, 1.00 equiv) to afford 23.6 g (96%) of the product as a light yellow oil.
  • the method used to prepare 206 was used with the compound from the previous step (2.3 g, 5.67 mmol, 1.00 equiv) and N-methylpiperazine (850 mg, 8.50 mmol, 1.5 equiv) to afford 2.3 g (83%) of PH-IMA-2013-003-384-8 as a yellow oil.
  • the method used to prepare 211 was used with the compound from the previous step to afford 1.8 g of the product as a yellow oil.
  • the method used to prepare 211 was used with the compound from the previous step (1.8 g, 4.63 mmol, 1.0 equiv) and 4-(1H-1,2,3-triazol-1-yl)benzoic acid (875 mg, 4.63 mmol, 1.0 equiv) to afford 1.7 g (66%) of the product as a yellow solid.
  • the method used to prepare 203 was used with the compound produced in the previous step (500 mg, 1.63 mmol, 1.00 equiv) and 4-(pyridin-2-yl)benzoyl chloride (393 mg, 1.81 mmol, 1.10 equiv), to afford 360 mg (45%) of the product as a yellow solid.
  • the method used to prepare 206 was used with the compound produced in the previous step (360 mg, 0.74 mmol, 1.00 equiv) and 1-methylpiperazine (111 mg, 1.11 mmol, 1.50 equiv) to afford 300 mg (71%) of the product as a yellow solid.
  • the method used to prepare 210 was used with the compound produced in the previous step (300 mg, 0.53 mmol, 1.00 equiv), affording 88.8 mg (32%) of the product as an off-white solid.
  • the method used to prepare 209 was used with the compound produced in the previous step (1.31 g, 6.12 mmol, 1.00 equiv) to afford 0.7 g (57%) of as a white solid.
  • the method used to prepare 211 was used with the compound produced in the previous step (250 mg, 0.50 mmol, 1.00 equiv) to afford (70%) of as a yellow foam.
  • the method used to prepare 210 was used with the compound produced in the previous step (200 mg, 0.35 mmol,) to afford 15 mg (8%) of 135 as an off-white solid.
  • the method used to prepare 1 was used with the compound produced in the previous step (500 mg, 2.46 mmol, 1.00 equiv) to afford 250 mg (99%) of the product as a colorless oil.
  • the method used to prepare 206 was used with the compound produced in the previous step (1.075 g, 2.64 mmol, 1.00 equiv) and 1-(d 3 )-methylpiperazine (300 mg, 2.91 mmol, 1.10 equiv) to afford 650 mg (50%) of the product as a yellow oil.
  • the method used to prepare 210 was used with the compound produced in the previous step (850 mg, 1.51 mmol) to afford 112.2 mg (14%) of 137 as a light yellow solid.
  • the method used to prepare 206 was used with the compound produced in the previous step and (2S)-5-[[(1R,2S)-2-(4-fluorophenyl)cyclopropyl](prop-2-en-1-yl)amino]-2-[[4-(1H-1,2,3-triazol-1-yl)phenyl]formamido]pentanoic acid (300 mg, 0.63 mmol, 1.00 equiv) to afford 150 mg (42%) of the product as a colorless oil.
  • the method used to prepare 210 was used with the compound produced in the previous step (150 mg, 0.26 mmol) to afford 65.7 mg (47%) of 138 as a white solid.
  • the pH value of the solution was adjusted to 2 with HCl (2 M ).
  • the resulting solution was extracted with 3 ⁇ 150 mL of EtOAc, and the organic layers were combined, washed with 1 ⁇ 300 mL of brine, dried over Na 2 SO 4 , concentrated under vacuum, and applied onto a silica gel column with CH 2 Cl 2 /methanol to afford 4.5 g the product as a off-white solid.
  • the method used to prepare 208 was used with the compound from the previous step (300 mg, 0.75 mmol, 1.00 equiv) to afford 200 mg (67%) of the product as off-white solid.
  • the method used to prepare 205 was used with methyl (5S)-6-(4-methylpiperazin-1-yl)-6-oxo-5-[4-(pyrimidin-2-yl)phenyl)formamido]hexanoate (1 g, 2.28 mmol, 1.00 equiv) to afford 600 mg (62%) of the product as a colorless oil.
  • the resulting solution was allowed to react, with stirring, for an additional 12 h while the temperature was maintained at 80° C. in an oil bath.
  • the reaction mixture was cooled to room temperature and then quenched by the addition of 20 mL of water.
  • the resulting solution was extracted with 3 ⁇ 50 mL of EtOAc, and the organic layers were combined, dried over anhydrous Na 2 SO 4 , concentrated under vacuum.
  • the residue was applied onto a silica gel column with EtOAc/petroleum ether (1:100), affording 1 g (62%) of the product as a yellow oil.
  • the resulting solution was allowed to react, with stirring, for an additional 12 h while the temperature was maintained at 90° C. in an oil bath.
  • the reaction mixture was cooled to room temperature, then diluted with 50 mL of EtOAc.
  • the resulting mixture was washed with 30 mL of H 2 O, dried over anhydrous Na 2 SO 4 , then concentrated under vacuum.
  • the residue was applied onto a silica gel column with EtOAc/petroleum ether (1:100), affording 350 mg (64%) of the product as a yellow oil.
  • the method used to prepare 206 was used with the compound produced in the previous step (5 g, 9.00 mmol, 1.00 equiv) and thiomorpholine-1,1-dioxide (1.46 g, 10.8 mmol, 1.20 equiv) to afford 1 g (17%) of the product as a yellow oil.
  • the method used to prepare 207 was used with the compound from the previous step (1 g, 1.49 mmol, 1.00 equiv) to afford 300 mg (46%) of the product as a yellow oil.
  • the method used to prepare 208 was used with the compound from the previous step (50 mg, 0.11 mmol, 1.00 equiv) to afford 45 mg (91%) of the product as a light yellow solid.
  • the method used to prepare 207 was used with the compound from the previous step (5 g, 7.17 mmol, 1.00 equiv) to afford 1.7 g of the product as an off-white solid.
  • the method used to prepare 208 was used with the compound from the previous step (1.7 g, 3.71 mmol) to afford 1.2 g (71%) of the product as a yellow solid.
  • the method used to prepare 204 was used with the product from the previous reaction (1.4 g, 2.37 mmol, 1.00 equiv) to afford 1.5 g (92%) of the product as a yellow solid.
  • the method used to prepare 211 was used with the product from the previous step (397 mg, 0.85 mmol, 1.00 equiv) and 4-(2,5-dimethyl-1H-pyrrol-1-yl)benzoic acid (200 mg, 0.93 mmol, 1.10 equiv) to afford 200 mg (35%) of the product as a yellow oil.
  • the method used to prepare 1 was used with the product from the previous step (120 mg, 0.18 mmol, 1.00 equiv) to afford 12 mg (10%) of the product as a light yellow solid.
  • Example 158 was prepared by Flash-Prep-HPLC. This resulted in 65 mg (23%) of Example 158 as a yellow solid.
  • Example 158 and its bis-tosylate salt may be prepared by the following method.
  • the method used to prepare 201 was used with the compound from the previous reaction (3 g, 0.015 mol, 1.00 equiv). The crude product was used for the next step without further purification.
  • the method used to prepare 206 was used with the product from the previous step (1.9 g, 5.56 mmol, 1.00 equiv) and thiomorpholine-1,1-dioxide (1.13 g, 8.34 mmol, 1.50 equiv), to afford 1.4 g (55%) of the product as a brown solid.
  • the method used to prepare 212 was used with the product from the previous step (800 mg, 1.8 mmol, 1.00 equiv) to afford 550 mg (71%) of the product as a brown solid.
  • the method used to prepare 208 was used with the compound from the previous step (550 mg, 1.27 mmol, 1.00 equiv) to afford 350 mg (64%) of the product as a off-white solid.
  • the method used to prepare 206 was used with the product from the previous step (2 g, 6.02 mmol, 1.00 equiv) and thiomorpholine-1,1-dioxide (1.22 g, 8.96 mmol, 1.49 equiv) to afford 1.4 g (52%) of the product as a yellow oil.
  • the method used to prepare 205 was used with the compound from the previous step (1.4 g, 3.11 mmol, 1.00 equiv) to afford 1 g (74%) of the product as a white solid.
  • the method used to prepare 202 was used with the compound from the previous step (900 mg, 2.07 mmol, 1.00 equiv) to afford 450 mg (52%) of the product as a yellow oil.
  • the method used to prepare 208 was used with the compound from the previous step (450 mg, 1.07 mmol, 1.00 equiv) to afford 300 mg (67%) of the product as a yellow oil.
  • the method used to prepare 206 was used with the compound from the previous step (2.7 g, 8.15 mmol, 1.00 equiv) and thiomorpholine-1,1-dioxide (1.34 g, 9.84 mmol, 1.21 equiv) to afford 1.8 g (49%) of the product as an off-white solid.
  • the method used to prepare 205 was used with the compound from the previous step (1.8 g, 4.01 mmol) to afford 1.22 g (70%) of the product as an off-white solid.
  • the method to prepare 202 was used with the compound from the previous step to afford 0.8 g (68%) of the product as an off-white solid.
  • the method used to prepare 208 was used with the compound from the previous step (800 mg, 1.90 mmol, 1.00 equiv) to afford 480 mg (60%) of the product as a off-white solid.
  • the method used to prepare 206 was used with the compound from the previous step (1.7 g, 4.95 mmol, 1.00 equiv) and thiomorpholine-1,1-dioxide (800 mg, 5.87 mmol, 1.19 equiv), to afford 1.35 g (59%) of the product as a light yellow solid.
  • the method used to prepare 205 was used with the product from the previous step (1.35 g, 2.93 mmol, 1.00 equiv) to afford 0.98 g (75%) of the product as a off-white solid.
  • the method to prepare 210 was used with the compound from the previous step to afford 41.5 mg (30%) of the product as a light yellow solid.
  • N-[(2S)-5-[[(1R,2S)-2-(4-fluorophenyl)cyclopropyl](prop-2-en-1-yl)amino]-1-(4-methylpiperazin-1-yl)-1-oxopentan-2-yl]-4-(pyrimidin-2-yl)benzamide (520 mg, 0.91 mmol, 1.00 equiv), THF (15 mL), 1,3-dimethyl-1,3-diazinane-2,4,6-trione (426 mg, 2.73 mmol, 2.99 equiv), Pd(PPh 3 ) 4 (210 mg, 0.18 mmol, 0.20 equiv).
  • MS-triggered preparative HPLC The resulting residue was purified by MS-triggered preparative HPLC to afford 7.TFA (100 mg, 14%) as a brown red gum.
  • MS-triggered Preparative HPLC purifications were performed using a Sunfire C18 column, OBD, 10 ⁇ (30 ⁇ 250 mm) with UV detection at 220 nm using a solvent gradient program (15% to 55% acetonitrile/water with 0.1% trifluoroacetic acid).
  • the resulting solution was stirred for 1 h at 0° C. in a water/ice bath.
  • the pH value of the solution was adjusted to 2 with hydrogen chloride (2 mol/L).
  • the resulting solution was extracted with 3 ⁇ 100 mL of ethyl acetate and the organic layers combined.
  • the resulting mixture was washed with 1 ⁇ 100 mL of brine.
  • the mixture was dried over anhydrous sodium sulfate.
  • the resulting mixture was concentrated under vacuum.
  • the resulting mixture was washed with 20 mL of DCM.
  • the solids were filtered out. This resulted in 3 g (70%) of (2) as yellow oil.
  • the resulting solution was stirred for 16 h at 25° C. The solids were filtered out. The resulting mixture was concentrated under vacuum. The resulting solution was diluted with 100 mL of H 2 O. The resulting solution was extracted with 3 ⁇ 100 mL of ethyl acetate and the organic layers combined and dried over anhydrous sodium sulfate. The residue was applied onto a silica gel column with ethyl acetate/petroleum ether (1:3). The collected fractions were combined and concentrated under vacuum. This resulted in 2.5 g (70%) of (3) as yellow oil.

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